Could it be due to the checking of SPAM? Have the first 2k of the message viewed for spamhalter. 

500 e-mails incoming to the 'main folder' which stops automatic checking after 750, plus spamhalter looking at the message (modified to the first 2048 bytes, not the full message) could be  a real drag on opening the folder.

of course may be far off in my guess. 

I travel a lot and when I get over 500 new emails (two days worth for me), Pegasus has always taken a long time once they are downloaded to give me control (I get just an hour glass or Windows 7 'please hold' circle :))

I am running 4.63 and the latest version of IERenderer (the 3/2012 release) if add-ons matter.  It was doing this with BearHTML as well.

Not a huge inconvenience and perhaps something with my config if anyone can tell me where to look.

I am gone a week plus it's a long long time before I can start reading.

also as they are downloading, I can read and delete/move/etc just fine...it's only when the download completes that I get locked up.

Perhaps it's the interaction with the email server and deleting the downloaded mail from there.