Bug: Wordcount off by several thousand.

I downloaded the beta, installed it, and opened up my current project into a new instance. The wordcount it is giving is off by about 5,000.

Scrivener 1.0.7.0 reports the wordcount at 60,057. My compiled Word document reports 60689 (the extra words likely come from chapter headings, hyphenation, etc). But 2.9.0.3 reports a wordcount of 55897 which feels very off, and I don’t appear to be missing any scenes.

I figured I should report the discrepancy. When I searched I didn’t see any other wordcount-related bugs.

The project is saved to Google Drive folder.
Beta 3, version 2.9.0.3 (64bit)
This is an admin account and I don’t have any other backup or special security stuff.

Follow-up: I’ve made some small edits to the file and it thinks I’ve somehow lopped off around 4,000 words both yesterday and today. I suspect the bug is related to this:

Interestingly, while I’ve only really deleted about a hundred words, and Scrivener thinks I’ve deleted about 4,000 since yesterday, the global wordcount has gone up since yesterday to 57,858.