gurov,
What I think is going on isn't really a code problem at all, instead it's a conceptual design limitation.
When you shift from PNR to Drive, the function of the shift lever changes. In PNR, the lever sets the gear, with no ambiguity - the selected gear follows the lever position. However, when you shift to Drive, the lever doesn't set the gear at all, it just sets the highest allowed gear (5th in your case). The controller doesn't know if you want 5th, or 4th, or 3rd, or 2nd or 1st.
In the older codes, the first gear to come up was the highest gear, so the controller used that, then downshifted based on the current rpm and the uner-rev limiting algorithm into first (the clunking down the gears you described). However, in the new code, the logic was tightened up, exposing the confusion over what gear the controller should aim for. As a result, the code becomes very confused if you are in manual mode on a shift from PNR to Drive.
In auto mode, on a shift to Drive the target gear is then grabbed from the shift table, the appropriate gear is selected, and all is well.
However, if you are in manual mode when you shift from PNR to Drive, the code has to know what gear to shift to. The code used to assume you wanted first, but users (including you perhaps) didn't like that behavior (it was throwing the trans into 1st at speed if there was a reset). This could also happen if the user was coasting down a hill in neutral, then shifted into gear (not recommended, but some people do it). So the gear was left undefined. However, undefined is a bad thing for the control logic!
This was the reason I originally prevented the use of manual mode in start-up, but it took a long time for me to remember that (so I am sorry for advising you that you could try manual mode for start up simply by editing the INI - I believe no-one else did this, and that's why no-one else was seeing the problem you reported).
In theory, we could have an algorithm to select an appropriate gear when entering Drive, but that's exactly what the auto-mode is, and it seems inefficient to have a separate mode for just that.
So the codes I will release in the next few days will revert to auto_mode any time you shift to PNR, and will prevent the user from overriding the selection of sequential or skip shift auto_modes for start up. Users will have to select manual mode only once they have moved the shift lever to a forward gear position. This way there is no confusion for the controller over what the current gear should be.
However, if it helps at all, I have added the function you requested where the first press of a shift button changes the mode from auto to manual, and only the second and subsequent presses actually shift gears. That way if you are in auto mode and first gear (or any other forward gear) a press of either shift buitton will put you in manual mode, but leave the trans in the same gear (first in this case). The second press of either shift button will then change the gear.
The code is done, but I need to do a bit of testing before releasing them (they will be 2.105 and 4.004, announced in the "Latest Code Updates" thread:
viewtopic.php?f=4&t=20 )
Lance.