I received a response from CrashPlan:
Thank you for contacting our Champion Support Team.
It looks like the CrashPlan app is restarting your backup unexpectedly, it is actually running a file verification scan. The scan puts ALL of your data in the To Do list. Then as the backup after the scan runs, its analyzes your files to determine if it has been backed up before and can be skipped, or if its new/changed and needs to be backed up. The percentage complete that you see is CrashPlan's progress through the current To Do list, not the overall backup.
The scan is an important and normal part of CrashPlan's scheduled activities, but it can also be triggered by several events. To read more, click on the link below:
The explanation for the lengthy time estimation relates to how CrashPlan prioritizes files for backup. CrashPlan backs up your most recent changes first. When the scan finds new files for backup, these files go straight to the top of CrashPlan's “to do” list. This impacts the estimated time to complete backup because the estimate is based on the type of files the scan is reviewing (i.e., new or existing) and your current network speed.
If you have any further CrashPlan questions or concerns, or need clarification please do not hesitate to reach out.
Champion Support Specialist"
This seems to be the case. The number of files sent match up but the total percentage is still off even after a FULL manual file scan. (that normally only happens every 30 days)
Things should sort themselves out over time after the complete verification "To Do" list is done.