Sync app updates to iPad via USB: takes several tries; and weird automatic app deletions

Two odd sync behaviors--maybe connected, maybe not:
1. Since updating to iOS 5 (and/or the version or two of iTunes) iTunes no longer syncs all my apps (updated on the Mac) to the iPad when I plug in. (I'm not using any kind of auto-downloading or iCloud; not enough space on the iPad for that. Nor am I using WiFi sync--just plain old plug-and-go.)
It syncs a few apps and gives no error, but then I notice that some apps remain non-updated. So I sync again... and a few more apps transfer. After 3-5 syncs, all my apps are up to date. Every time, unless it's just 1 or 2 updates, I must sync repeatedly.
2. I'm set to sync manually only (not automatically when connected). So I click Sync, and the Sync button immediately turns to an Apply button--even though I have not changed anything. Then, after the sync (or syncs plural!) if I try to click away from the iPad panel to other parts of iTunes, OR if I try to quit iTunes, it asks if I want to Apply or cancel my changes. Umm... what changes? So I say Apply and it tells me it's going to delete some apps! (Apps which are indeed present on the Mac still, and which I want to keep.) So I cancel and all is well, except it's annoying, and risky if I ever accidentally do Apply. (I don't want to lose game progress or app data.) There's no space warning; I have ~2GB free and the apps it offers to remove seem pretty random to me.
So every time I'm done syncing, I must cancel the "Apply" for app removals I never asked for.
However, I AM still able to safely make changes I do want to apply: I must do them before the first sync, and then when I sync the changes (adding/removing apps, books, music, whatever) work just fine. Then afterward comes the Apply offer (deletion of apps) which I cancel.
Any ideas on these issues?
I wiped the iPad and restored from backup; no difference. The iPad and iTunes are fully updated; no difference. (This happened through at least the last two versions of iTunes.) The Mac itself is running Leopard, but it does meets iTunes' requirements.
Thanks in advance!

Two odd sync behaviors--maybe connected, maybe not:
1. Since updating to iOS 5 (and/or the version or two of iTunes) iTunes no longer syncs all my apps (updated on the Mac) to the iPad when I plug in. (I'm not using any kind of auto-downloading or iCloud; not enough space on the iPad for that. Nor am I using WiFi sync--just plain old plug-and-go.)
It syncs a few apps and gives no error, but then I notice that some apps remain non-updated. So I sync again... and a few more apps transfer. After 3-5 syncs, all my apps are up to date. Every time, unless it's just 1 or 2 updates, I must sync repeatedly.
2. I'm set to sync manually only (not automatically when connected). So I click Sync, and the Sync button immediately turns to an Apply button--even though I have not changed anything. Then, after the sync (or syncs plural!) if I try to click away from the iPad panel to other parts of iTunes, OR if I try to quit iTunes, it asks if I want to Apply or cancel my changes. Umm... what changes? So I say Apply and it tells me it's going to delete some apps! (Apps which are indeed present on the Mac still, and which I want to keep.) So I cancel and all is well, except it's annoying, and risky if I ever accidentally do Apply. (I don't want to lose game progress or app data.) There's no space warning; I have ~2GB free and the apps it offers to remove seem pretty random to me.
So every time I'm done syncing, I must cancel the "Apply" for app removals I never asked for.
However, I AM still able to safely make changes I do want to apply: I must do them before the first sync, and then when I sync the changes (adding/removing apps, books, music, whatever) work just fine. Then afterward comes the Apply offer (deletion of apps) which I cancel.
Any ideas on these issues?
I wiped the iPad and restored from backup; no difference. The iPad and iTunes are fully updated; no difference. (This happened through at least the last two versions of iTunes.) The Mac itself is running Leopard, but it does meets iTunes' requirements.
Thanks in advance!

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