I just read through this entire thread (not that it's THAT long) and see some things that haven't been addressed:
When using Google's mail client on your BB for a Google Apps account, you should be using "Mail by Google", not "Gmail". You can download/install Mail by Google using by going here:
http://m.google.com/a
When using POP3 to get your mail in BIS, deleting a message "on Mailbox & Handheld" actually
DELETES the message on the server. There is no way to
ARCHIVE the server copy from the native BB mail app.
When using IMAP to get your mail in BIS, deleting a message "on Mailbox & Handheld" actually
ARCHIVES the message on the server. There is no way to
DELETE the server copy from the native BB mail app.
Though I appreciated the read-status synchronization, and wasn't really bothered by the IMAP delays the archive/delete functionality drove me back to POP3 once I realized what was going on.
Also... when using IMAP, the Gmail mailbox is polled every 15 minutes. If new mail has arrived since the last poll, the polling interval is reduced to 3 minutes. If no new mail arrives for 5 successive polling cycles, the cycle is increased to 15 minutes. Polling ceases when the device is turned off. Polling is resumed when the device is powered back on, however receipt of mail during this polling cycle does not trigger a reduction in the polling interval unless the received mail actually arrived in the mailbox within the previous 15 minutes. This information is based on my own experience and confirmation via the "last account activity" link at the bottom of the Gmail main screen.