I can't dock Adobe Reader windows with AquaSnap

This is a known issue which is caused by Adobe Reader itself. For security reasons, the recent versions of Adobe Reader use a sandbox that isolate Adobe Reader from other applications like AquaSnap. The solution to this problem is to disable this sandbox.

To do this on Adobe Reader X:

1. Open Adobe Reader.
2. Choose Edit > Preferences.
3. In the Categories list on the left, select General.
4. Disable Enable Protected Mode at startup.
5. Restart Adobe Reader.

To do this on Adobe Reader XI:

1. Open Adobe Reader.
2. Choose Edit > Preferences.
3. In the Categories list on the left, select Security (Enhanced).
4. Disable Enable Protected Mode at startup.
5. Restart Adobe Reader.

You can find out more about the protected mode of Adobe Reader on  this page.