Hello DarkStar
This morning I have done some tests.
I install a new portable Reaper (Evaluation version) on XP; nothing is changed in preferences. With this I redo the test on both a XP and a Windows 7 PC with the same midi file; it gives the same results: no SysEx messages.
Looking to the difference between your latest picture on the forum and my piano roll editor, your picture contains much more notes (events). After some experiences I discover that you insert my 4 channel midi file with the option "Multichannel item on a single track" while I do the other option "Single channel items on multiple tracks".
In your case you have SysEx commands in the Reaper editor, in my case not.
I have chosen the "Single channel items on multiple tracks" option because the Hauptwerk organ simulator has more channels; each channel is for a organ manual or pedal. You can play on a manual and pedal and a solo voice on an other manual. In my case there are 4 manuals.
In case with each manual on his own channel in Reaper, it's easier for me to see and to edit notes on the different organ manuals comparing with the score.
I continue the test with inserting the midi file with the "Multichannel item on a single track".
I have exported this "single track" midi file (see attachment) and test this with my organ. It doesn't work correctly. I discover that Reaper shuffles the Non-Reg Parm LSB, NRP MSB and the Data Entry MSB.
See picture
https://dl.dropboxusercontent.com/u/...%20file%29.jpg. The start is different comparing the pictures, attached in my first topic and near event 42/43 the MSB (99) parameter is not in the exported midi file.
Questions:
1) is my way of handling the midi file wrong?
2) is there a bug in Reaper with the cc messages after a SysEx message (it shuffle items) as shown in the start of my midi file?
3) is there a solution to do it in my way using "Single channel items on multiple tracks" without the SysEx problem?
4) or is it a bug in Reaper that in case of a multi channel midi file and using the "Single channel items on multiple tracks" option kills all SysEx events?