Note in my setup on running on exchange so there are more than likely some differences in implementation but here's hoping this is of some help.
I had somthing similar when runnig BES 5 SP1, in SP1 seting up TCP Ping was a royal pain in the arse. I opened my case with RIM and reviewed my config and I had a typo in the config files, once addressed all was well. SP2 introduced a GUI for setting TCP Ping, so if you're not running SP2 I woudl strongly reccomend upgrading & letting it implement TCP ping properly.
Apart from that I the only other things I can think of are:
make sure you read the install prerequisites and implemented properly, if you dont' you'll have simialr issues (E.G. If IPV6 is enabled it will cause you tonnes of pain).
Consider doing a full BES shutdown (power off both nodes) let one warm up fully then power on the seconffand let it do the same (after you've confirmed install prerequisites of course).
If you're still getting partition singleton issues you will really want to consider contacting RIM (or your carrier if they have BES support - Rogers in canada offers free bes support for their customers, not sure about carriers the US) support to get them to take a look at your setup as somtimes lots of little things can get in the way.
Hope this helps and good luck.
Z
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