Okay I've disabled IMAP (which apparently is enabled by default); POP has never been enabled.
The problem is continuing, with as I say perhaps a dozen messages a day (out of hundreds) not appearing in the Inbox.
Note that I have the SmartLabels lab enabled, and the issue appears to only happen to e-mails which arrive from Yahoo Groups mailing lists. While a great many Yahoo Groups messages do properly show up in the Inbox, those that don't seem to always get misclassified by SmartLabels as "Bulk" instead of properly appearing under "Forums." Thus, the issue seems to me to be a side-effect of SmartLabels.