Both of these are interesting symptoms that shouldn't be happening...
On the "3 hours and stopped", what packet type are you using? You'd probably have reported this, but are you seeing an engine errors listed above the time graph? If not, have you changed the [Advanced] "ShowErrorPanel" setting in your ini file to supress any errors?
When outsanding requests exceeds the listed outstanding requests (Edit -> Options, Packet options, Maximum concurrent requests), then PingPlotter skips the trace (it won't send out any more packets until some have completed). It sounds like there is some sort of condition that is causing packets to *never* complete (which would certainly be a bug). Each of the 3 packet types have separate queus for this - ICMP, UDP and TCP. They also each have slightly different logic for determining that a packet is "done". If you change packet types once this condition has been reached, things should start working again (although this doesn't repair the situation internally, it just starts looking to a new "engine" instance for being overloaded). If you switch back to the original packet type, this will stop working again.
OK, so information I need on this one:
1) What packet type are you using?
2) Are you seeing any engine related errors on the main screen, above the time graph. If not, is your ini file setting supressing those error messages? If you're supressing them, please unsupress them so we can get to the bottom of this.
I've run into the situation using the TCP ping engine only - when I suspend my computer, then resume it, things don't recover correctly (corner cases aren't always fully flushed out on beta versions, unfortunately).
Do you have any idea what version first exhibited the "13 seconds on close" problem? If you have another PC available to try this on, do you see similar symptoms, or is it isolated to this machine specifically?
Just a quick open / close causes this pause to happen? (I'm trying to figure out what logic paths happen every time where a "wait" condition would be introduced that takes CPU). This could be a problem the version check logic - are you set to have PingPlotter automatically check for new versions? If you do a manual version check (Edit -> Options, Internet, Version checking, "Check Now" button), does the status bar show "You have the latest pre-release version of PingPlotter", or does it stay blank?
Thanks (as always) for the reports, Jason!
P.S. I'm moving this post to the beta forum.