Long scratches are likely to be something rubbing as you suggested, checl the rubber guides for debris.
As for the window not going up automatically, that's a safety feature. It's detecting some resistance (like little fingers in the window) and reversing. It could be something in the alignment, maybe it's only slightly out so happens when it's hot or cold and warped in just the right way, or there is debris in there!
The other option is your battery isn't charged enough. I found that when my battery got too low the windows would not auto wind up, especially if the car wasn't running. If you haven't repalced the battery yet, it's getting to that age.
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