I have the same problem, but i hope that problem will be fixed if I buy the heart-rate monitor Zephyr™ HxM which logs the movement even without a GPS signal?
I just did a trial run with Run.GPS on my Android phone and it looks like the GPS resolution got quite bad during the run (by the way, it's "resolution", not "dilution"... get a better German-English dictionary :)). The problem is that these phases are now shown as pauses, when in fact I did keep running the whole time. If you look at the activity graph and the GPS resolution statistics, you have corresponding bad resolution whenever there was no recorded activity. It would make a lot of sense if Run.GPS could detect these situations and automatically create an average for these gaps.