Recently (since Gingerbread - OTA ???), when I delete emails from my phone, they do not get deleted from gmail if I log in on a pc. Likewise, if I read them on my phone, they show up as not read on gmail via the pc. On my phone, I'm using the standard gmail app, which has always worked in the past.
I do still get all emails on my phone. I have gone into settings, accounts, and made sure that syncing is checked and have refreshed from in gmail on my phone. No changes.