1. The list is truncated because of a limit in SQL server. IIRC it has to do with the number of function parameters and there isn't a work around.
2. Maybe using automatic transitions that only operate on drawings? Just thinking out loud here, maybe someone else will chime in.
I suggest you contact your VAR to get help from SolidWorks tech support with these issues.
You need to have dual transitions. The transition you are using for your notifications, use a rule. In the OR statement, include .SLDDRW as the only file you want to view. The statement needs to be written inside the OR folder. The "TYPE" should be Filepath....The argument should be %.SLDDRW.
Hope this helps.