Recently we've faced with situation when MSBUILD version was changed 4.0 - 14.0 and our code coverage statistics was dropped (dotCover, source code, etc. remained the same).
After some investigations we figured out that source code was analyzed in different way (probably IL was changed and dotCover provided other results). It's not clear why we obtained new results since code was not changed.
We've created a sample project to let you reproduce it on your side. As for example of issues we noticed, please take a look at these ones:
Before (4.0):After (14.0):
Please clarify this behavior because it looks like a bug. Otherwise suggest your solution how to resolve this situation in order to provide the same statistics values that were before the change MSBUILD version to 14.0