For some time I use exclusively MapInstall with all kind of maps: native Garmin, cgpsmapper, mkgmap. I have never noticed problems.
Actually I don't send maps to GPS, I use a virtual GPS which is a directory on my HDD. MapInstall can perform some more processing on real GPS. It can create single gmapsupp.img or multiple img with names corresponding to map name and can split maps between internal memory and SD. Maybe there are some problems in this case.
There is one case, where MapInstall really doesn't create img. It is when one compiles a new version of own map without changing tiles ID. In this case MapInstall assumes, that map is already installed and doesn't update it.