(The problem occurs regardless of running in UI or batch mode).
I am trying to generate by command line the opencov archive but it does not correctly generate the fullPath field if the files it parses are under /Packages, example (using the sample that comes with the CodeCoverage package):
If instead I leave it where it was originally if it does well:
As a workaround, you could use pathReplacePatterns coverage option in batchmode to transform relative path back into full path. Something like pathReplacePatterns:./,C:/MyProject/ should do the trick. You can find more details here.