My experience is that when doing an incremental backup, that SuperDuper copies files across to the backup first, before deleting the outdated files. So it is possible that if you don't have much HD space on the backup volume, which should be similar to the source), then SD can't copy the updated large image file onto the backup volume to start with. The solution was to delete a selection of files from the backup volume manually, right before performing the incremental backup. This happened to me quite a bit, and wasn't specific to Parallels. Although Parallels may aggravate the problem since the program -- by design -- works with large image files.
SuperDuper not working for me very well. Processes are very slow to setup and once things get rolling I get an "effective copy speed 0.59 MB/s". I've tried wirelessly across an Airport setup, directly connecting to an external FireWire drive and by putting the MacBook into Target Disk mode and running SuperDuper off a Dual Processor G5.
Airport is great for http requests and email -- not sending large .hdd files. Remember -- starting up in safe mode might solve a lot of problems here. When you put the MBP into TDM -- does this work, or not?