The "PHP coverage thingy", which is called PHP_CodeCoverage btw., currently only supports line coverage. This is why its Clover XML reporter sets "conditionals" and "coveredconditionals" to 0. In the near future, Xdebug will provide statement coverage and branch coverage information. This will then be used by PHP_CodeCoverage to set "conditionals" and "coveredconditionals" properly.
That being said, it seem that the patch mentioned above somehow makes the weather report think that something is wrong with condition coverage. It would be nice if someone could look into this. I will try to reproduce the issue and, if need be, open a separate ticket for this with more detailed information.