I've seen problems like this with my Time Capsule, too, but with scheduled runs of another program (not SD!) that only does folder synchronization. Syncs with that program fail if Time Machine starts accessing the Time Capsule first.
Haven't figured it out, but it seems to be something to do with the fact that if a Time Machine backup is running, a second 'volume' appears in the /Volumes folder with '-1' appended to its name: somehow this gives Time Machine the protection it needs but also lets you access files on the Time Machine in Finder--but spoils access for other programs because the file path names that were set don't work with the '-1' appended name.
In fact it was for this reason that I stopped trying to run SD! backups to disk images on the Time Capsule; I also have a simple NAS which works fine, so I still use that instead if I need to backup to a network disk image.
[edit]
More information about Time Capsule's multiple identities here:
http://discussions.apple.com/thread....977&tstart=176