I have similar problems and I’m assuming since a lot of people use the Garmin Vista HCX or similar models that do not store number of satellites,hdop or another quality indicator there should be others that have to deal with the same issue.

As you described, getting rid of the temporary signal loss can be accomplished wuth gpsbabel, while the scribble thing is harder to come by. I’ve been removing these manually (with GPSprune - but there are quite a few tools out there).

Something automatic would be nice too. Besides the scribble effect, from time to time the signal is picked up partially and the location wanders off in a straight line sometimes several hundred meters (can be seen in the lower image, once towards 11 o clock, once towards 4 o clock.