Shutting down or restarting my Pre causes software to change and limit email/text/contact functionality.

Hi all,
I just got back from a two week vacation, which happened to be just about a week after 1.4.  First off, before my vacation, I noticed a couple of weird things happening:
Universal search wasn't working, except for applications and phone numbers.  So if I slid open my phone and started typing, I'd get no contact results and no option to search the web/wikipedia/etc.  Searching for something like "contact" would bring up a result for the contacts app though
Clicking on the messaging app would register on the screen like I had clicked on it and it was about to open up, but it would never actually follow through.  It didn't lock the phone up, it just registered that you had clicked on it and never did anything about it.  This meant no messages of any sort, including text messages .
Certain folks phone numbers had disappeared.  Not everyone, but a few scattered throughout.  Their contact information remained, just sans phone number.
When opening the email application, am greeted with simply a white page, and the +app button in the lower left.  Going to accounts, my two emails accounts aren't accounted for at all( gmail and a work imap ).  Unable to re-add either account.
So I figure something's gone wonky in the 1.4 update and that before I go off traveling for two weeks, I'll just hard reset it to make sure everything works.  I do that, everything seems to work fine, grab my spare battery and I'm off.  Unfortunately, no luck.  I'm in Washington DC and all the same problems are popping up.  Especially bad not being able to get text messages.  Fortunately, internet and the phone application work.  I took it in to a repair store, and they told me I was going to need to replace my phone, but they wouldn't be able to get one to me until after I had already went off to NYC.
So I get to NY, my phone still isn't working - though all of the above problems aren't totally consistent.  Sometimes it seems like everything is working.  Sometimes all of the problems are happening at the same time.  I run the diagnostic tests and get a result of 100- bad memory.  So I finally get a new phone from Sprint in Brooklyn, and get everything set back up.  Hurray for the cloud and palm profile here - saved me oodles of time and was pretty close to seamless.  Except for the random deleted phone numbers.  Anyway, everything seems to be working fine, no issues.  My battery ends up running low on me later that night, so I shut it down and put in my backup battery.
Bam! Back to the same issues.  Now mind you, this is on a new phone from Sprint( I watched him switch it over, so I'm certain they didn't just tell me I was getting a new one ).  The only things that are the same are my batteries, the back( it's a touchstone backpiece ) and my profile.  The issues seem to occur with both of my batteries, and the sprint guy seemed to think they were in ok shape.  I can't imagine it's the backplate, though I haven't tried with a different one yet.  So I'm left thinking it's my profile.
Now the odd part - very consistently after a reset my phone works beautifully.  The first time I shut it down or restart it the issues pop up and don't go away.  I've tried canceling all of my applications from loading, deleting all installed applications( installed via the app store only ), etc with no success.  It's kinda driving me nuts now.  It doesn't seem to be hardware based, the sprint store guys haven't been very helpful past replacing the phone the first time, and I'm not sure where to go next.
TL;DR: I'm having phone issues that appear to be related to my palm profile and am unsure as to how to go about solving them.
Thanks,
Ryan

Thanks for the help.
I've done as you've suggested and so far it seems to be working.  It's been about 30 hours now, I've drained the battery all they way down once, and when I get home this evening I'll try shutting down and switching to my backup battery just to double check that that works.  Otherwise, it certainly seems as if it's a profile issue.
So, if that is the case, is it going to be possible to get my contact information that was stored on my old profile?  I don't really use the calendar too much, so that's not a huge issue, but I would also like to get my paid apps back too if possible, or some sort of credit so I can buy them again.
Thanks again for the help,
Ryan
Edit: I just swapped out batteries and as expected, everything still works so does look like the profile.

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