I didn’t find a solution in this forum that helped in my situation, so I am posting this to help others that may have the same problem. I was working on it first in R5.11 and hoped my upgrade to R6 would help but it didn’t.
I finally found out my problem with not being able to pop certain accounts from Notes. After testing on my own and working with Lotus support, I realized the problem was too many unread documents. This was causing timeout issues. I marked my messages to “read” and was successful. I tested again by marking messages as “unread” and got to around 3,000 before I was getting timeout issues. I don’t know if attachments added to that delay.
I hope this helps someone else.