Yes, I've seen the issues you are describing.
I've only had issues with the Java Uploader since moving to IE7 (see note posted in red next to its link). I found that toggling between Pause and Resume seems to complete the processing and give it little nudges that report on the window when you use that bypass.
However, as a PC user, I prefer the Drag and Drop uploader over the other two for ease of use.
Danno