We are also doing a load of work on this, I've been scoping the outputs on my unit on the test bench, with Jorgen's help last night we did some diff's on various configs and are trying to see what exactly caused the problem.
Your original configs (The ones that you sent on Thursday) are going to be studied carefully this weekend by Marcell who is doing a large number of tests across a range of triggers and configurations.
One thing that Jorgen said was that you should perhaps quit the firmware uploads, once the firmware is up its the changes to the configs and tables that change the way the system works, the firmware is static, its stored in flashmemory which cannot be changed apart from a reflash.
I'm not sure about the 6V dwell time to be honest, its something that I'll be looking at to try and understand and document, I know that there have been significant changes in 1.1.xx firmware regarding dwell time and the way that VEMS controls the coil charging based on RPM.