Random build error - plugin assembly compatibility check

Hi, I upgraded to last Unity 4.6.2p2 few day ago and since then I am getting

“Failed to check compatibility between assemblies ./Temp/StagingArea/Plugins/Metro/Poly2Tri.dll and ./Temp/StagingArea/Plugins/Poly2Tri.dll”

really often (Poly2Tri is one of my plugins). Problem is, I do not get it always, in 1 of 5 cases the build completes successfully. I was getting this error even on previous versions of Unity, but it was much less frequent.
I suppose, if there were a real problem with the plugin dlls, it would just never build, but since it builds sometimes, it is strange.
Both versions of the dlls were build using VS2013, editor version in standard Windows desktop mode, Metro version in WSA Universal mode (it is not CPU specific).
Is there anything specific, that should be set to both versions? Or how is the compatibility check performed, how can I find out, where is the problem?

Thanks for any help…

This bug has been fixed, should be available in this weeks patch release.