a.gemspec

Gem::Specification.new do |s|
  s.name = "A"
  s.version = "0.0.0"
  s.summary = "Gem A"
end

Gemfile

gem 'A', :path => File.expand_path('../../a', __FILE__)

overview.txt

+ bundle --version
Bundler version 0.9.25
+ cd b
+ bundle install
Using A (0.0.0) from source code at /private/tmp/bundler-issue/a Your bundle is complete! Use `bundle show [gemname]` to see where a bundled gem is installed.
+ ruby problem.rb
Expected: /private/tmp/bundler-issue/a
  Actual: /private/tmp/bundler-issue/a
     ***  So everything's okay
+ bundle lock
Your bundle is now locked. Use `bundle show [gemname]` to list the gems in the environment.
+ ruby problem.rb
Expected: /private/tmp/bundler-issue/a
  Actual: /private/tmp/bundler-issue/gems/A-0.0.0
     ---  So you see the problem
+ cd ..
+ rm -rf b/.bundle
+ rm b/Gemfile.lock

problem.rb

#!/usr/bin/env ruby

require 'rubygems'
require 'bundler'
Bundler.setup

expected_gem_path = File.expand_path("../../a", __FILE__)
actual_gem_path = Gem.loaded_specs.values.find { |ls| ls.name == 'A' }.full_gem_path

puts "Expected: #{expected_gem_path}"
puts "  Actual: #{actual_gem_path}"
if expected_gem_path == actual_gem_path
  puts "     ***  So everything's okay"
else
  puts "     ---  So you see the problem"
end

script.sh

#!/bin/bash -x

bundle --version

cd b
bundle install
ruby problem.rb # no problem

bundle lock
ruby problem.rb # problem

# reset
cd ..
rm -rf b/.bundle
rm b/Gemfile.lock

Looks like github strips the paths when it shows the filenames here. They are intact if you clone it, though.