I just tested some testing with the Vengeance on an LE (1.42).
My results seem to be similar to others with the Vengeance issues... When the left flipper is up...strange things seem to happen. However my results seemed a bit different...I think there may be 2 different issues. I will also add that my first few tests were 100% normal...it took a handful of games to get the unexpected results.
The quicker a ball trips the opto after a flipper is pressed the more likely that the machine is fail to record the opto being tripped found that holding the flipper and tripping the opto with a bit of a time lapse would register a hit strangely enough. To add to the strangeness when the flipper button was held, and a hit was registered, the machine failed to release the magnet until it timed out even though a 3rd ball was kicked out...
Someone else had mentioned a scoring issue by pressing the flippers while the balls are locked. I did see this once but I was unable to track down what exactly caused this issue.
Note that I have not tired the fix that nodyeliab metioned above yet, and I have had similar behavior with Vengance on all of the LE codes that have been released.