Songs disappearing from playlist when I plug iPhone in to my PC/iTunes

I'm not sure if iPhone or iTunes is the problem as they both recently died about 3 weeks ago. My phone died so I took it to Apple and they swapped me out for a new one. When I got home to install the latest back up, I realized I had no music in my iTunes account. Strange! So I have reinstalled all of my music, but now whenever I plug my phone in to my PC and iTunes is open, it erases several songs from my playlist on my phone. The song is still on my phone, just not in the playlist. It's a complete pain in the You Know What to set up a play list in a specific order, so I'm starting to get a little irritated. I am not sure why this is happening. And why only some songs? Is there a glitch in the new iTunes version?  Could something be wrong with my new phone? Or the new update I just did on my phone yesterday? Please help....

Perhaps this will help:
http://support.apple.com/kb/TS1538
Regards.

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