Here's what it sounds like to me:
By default Androidplot uses the main thread for rendering, which is fine for most plots with a few dozen points but with plots containing a few thousand points as you've experienced it takes time. While the main thread is engaged to render the plot the UI will not update - this includes updating progress bars.
Setting your plot to render using background mode should solve the issue. If you are using Androidplot 0.5.1 or later you can enable the background rendering thread by adding this to your plot's xml:
renderMode="use_background_thread"
Nick