Before when it finally died it continued futilely untill it hit the end and timed out. When you started again the start message was the one after the last one you got.
Now that the invalid page limit is there, if it's set to 20, it will stop after 20 but the start download number is that 20th message. So, if it stopped because of the 999 error there are 20 messages it would miss unless the start page was changed.
Perhaps the invalid page limit could check to see if its the 999 error and set the start page to the one after the last valid page downloaded, and if it's because of a break in the messages it would set it to the 20th msg after the last valid message.
Hmmm.. thats an interesting point. What makes it tricky is that the error returned by Yahoo ('invalid page') is the same message regardless of whether you've been kicked or whether the message is genuinely missing.
Lets imagine there is a sequence of 21 deleted messages & PGO auto-resets back to the first missed message. It'll loop indefinitely as it will always fail on the 20th message which will always be missing.
I recommend just letting it carry on & at the end use the 'Find missing messages' feature in the Groups list context menu.
Cheers,
Wilson.