Comments: ** Comment from web user: pranavkothare **
Don't know if anyone was facing the same issue, but the workaround in the mean time for me was to add the projectassembly flag.
For those using MSBuild you could do something like:
"C:\Program Files (x86)\WSPTools\WSPBuilderExtensions\WSPBuilder.exe" -projectassembly "$(TargetPath)"
Hope it helps :)