the original openFileMethod of my content provider and the two alternate methods I use instead

ContentProvider.java

// including the imports to for the sake of the io objects 

import info.guardianproject.database.sqlcipher.SQLiteDatabase;
import info.guardianproject.database.sqlcipher.SQLiteQueryBuilder;
import info.guardianproject.iocipher.File;
import info.guardianproject.iocipher.FileInputStream;
import info.guardianproject.iocipher.FileOutputStream;
import info.guardianproject.iocipher.VirtualFileSystem;


...


@Override
	public ParcelFileDescriptor openFile(Uri uri, String mode) throws FileNotFoundException {
	
		ParcelFileDescriptor fd;
		int match = sURLMatcher.match(uri);

		if (Log.isLoggable(TAG, Log.VERBOSE)) {
			Log.d(TAG, "openFile: uri=" + uri + ", mode=" + mode);
		}

		switch (match) {
		case MMS_SCRAP_SPACE:
			fd = getTempStoreFd();
			break;

		default:

			fd = openFileHelper(uri, mode);
		}

		return fd;
	}

	public static synchronized InputStream getEncryptedFileInputStream(Context context, Uri uri) throws FileNotFoundException {

		if (uri.getAuthority().startsWith("com.gryphn")) {
			Cursor c = context.getContentResolver().query(uri, new String[] { "_data" }, null, null, null);

			int count = (c != null) ? c.getCount() : 0;
			if (count != 1) {
				// If there is not exactly one result, throw an appropriate
				// exception.
				if (c != null) {
					c.close();
				}
				if (count == 0) {
					throw new FileNotFoundException("No entry for " + uri);
				}
				throw new FileNotFoundException("Multiple items at " + uri);
			}

			c.moveToFirst();
			int i = c.getColumnIndex("_data");
			String path = (i >= 0 ? c.getString(i) : null);
			c.close();
			if (path == null) {
				throw new FileNotFoundException("Column _data not found.");
			}

			
			

		        return new FileInputStream(new File(path));
			

		} else {
			return context.getContentResolver().openInputStream(uri);
		}

	}

	public static OutputStream getEncryptedFileOutputStream(Context context, Uri uri) throws FileNotFoundException {

		if (uri.getAuthority().startsWith("com.gryphn")) {
			Cursor c = context.getContentResolver().query(uri, new String[] { "_data" }, null, null, null);

			int count = (c != null) ? c.getCount() : 0;
			if (count != 1) {
				// If there is not exactly one result, throw an appropriate
				// exception.
				if (c != null) {
					c.close();
				}
				if (count == 0) {
					throw new FileNotFoundException("No entry for " + uri);
				}
				throw new FileNotFoundException("Multiple items at " + uri);
			}

			c.moveToFirst();
			int i = c.getColumnIndex("_data");
			String path = (i >= 0 ? c.getString(i) : null);
			c.close();
			if (path == null) {
				throw new FileNotFoundException("Column _data not found.");
			}

			return new FileOutputStream(path);
		} else {
			return context.getContentResolver().openOutputStream(uri);
		}

	}

PduPersister.java

private void persistData(PduPart part, Uri uri, String contentType) throws MmsException {
		OutputStream os = null;
		InputStream is = null;
		IOCipherFileChannel destinationFileChannel = null;
		IOCipherFileChannel sourceCipherFileChannel = null;
		FileChannel sourceNativeFileChannel = null;
		
		try {
			byte[] data = part.getData();
			if ("text/plain".equals(contentType) || "application/smil".equals(contentType)) {
				ContentValues cv = new ContentValues();
				cv.put(SecureCom.Mms.Part.TEXT, new EncodedStringValue(data).getString());
				if (mContentResolver.update(uri, cv, null, null) != 1) {
					throw new MmsException("unable to update " + uri.toString());
				}
			} else {
//				os = mContentResolver.openOutputStream(uri);
				os = (FileOutputStream) SecureComMmsProvider.getEncryptedFileOutputStream(mContext, uri);
				
				if (data == null) {
					Uri dataUri = part.getDataUri();
				
					if ((dataUri == null) || (dataUri == uri)) {
						Log.w(TAG, "Can't find data for this part.");
						return;
					}
//					is = mContentResolver.openInputStream(dataUri);
					is = SecureComMmsProvider.getEncryptedFileInputStream(mContext, dataUri);
					
					

					if (LOCAL_LOGV) {
						Log.v(TAG, "Saving data to: " + uri);
					}

					ByteArrayOutputStream baos = new ByteArrayOutputStream(is.available());
					byte[] buffer = new byte[256];
					for (int len = 0; (len = is.read(buffer)) != -1;) {
						baos.write(buffer,0,len);
					}
					
					os.write(baos.toByteArray());
					baos.close();
					
					
//					destinationFileChannel = ((FileOutputStream)os).getChannel();
//					
//					if(is instanceof info.guardianproject.iocipher.FileInputStream){
//						if (LOCAL_LOGV) {
//							Log.v(TAG, "transfer from Cipher to Cipher :  " + uri);
//						}
//						
//						sourceCipherFileChannel = ((FileInputStream) is).getChannel();
//						sourceCipherFileChannel.transferTo(0, sourceCipherFileChannel.size(), destinationFileChannel);
//						sourceCipherFileChannel.close();
//					} else {
//						if (LOCAL_LOGV) {
//							Log.v(TAG, "transfer from Native to Cipher :  " + uri);
//						}
//						
//						sourceNativeFileChannel = ((java.io.FileInputStream)is).getChannel();
//						sourceNativeFileChannel.transferTo(0, sourceNativeFileChannel.size(), destinationFileChannel);
//						sourceNativeFileChannel.close();
//					}
//					
//					destinationFileChannel.close();
					
				
				} else {
					if (LOCAL_LOGV) {
						Log.v(TAG, "Saving data to: " + uri);
					}
					os.write(data);
				}
			}
		} catch (FileNotFoundException e) {
			Log.e(TAG, "Failed to open Input/Output stream.", e);
			throw new MmsException(e);
		} catch (IOException e) {
			Log.e(TAG, "Failed to read/write data.", e);
			throw new MmsException(e);
		} finally {
			if (os != null) {
				try {
					os.close();	
				} catch (IOException e) {
					Log.e(TAG, "IOException while closing: " + os, e);
				} // Ignore
			}
			if (is != null) {
				try {
					is.close();
				} catch (IOException e) {
					Log.e(TAG, "IOException while closing: " + is, e);
				} // Ignore
			}
			if(sourceCipherFileChannel !=null){
				try{
					sourceCipherFileChannel.close();
				} catch(IOException e){
					Log.e(TAG, "IOException while closing: " + sourceCipherFileChannel, e);

				}
			}
			if(sourceNativeFileChannel !=null){
				try{
					sourceNativeFileChannel.close();
				} catch(IOException e){
					Log.e(TAG, "IOException while closing: " + sourceNativeFileChannel, e);

				}
			}
			if(destinationFileChannel !=null){
				try{
					destinationFileChannel.close();
				} catch(IOException e){
					Log.e(TAG, "IOException while closing: " + destinationFileChannel, e);

				}
			}
		}
	}