For the record, FL Studio struggles with data such as Mod Wheel, Aftertouch, and Pitch Bend. It handles them in a way unlike any other DAW I've owned or tried. For example if you want to copy a performance to another instrument, it will copy note on/off and velocity data but not MW,AT, or PB data. The steps needed to manually copy that data are quite frankly silly and it's the main reason why I've been looking at other DAWs like Waveform and Bitwig.
Anyway I'll run the test when I boot the studio. I use the MW on my midi controller when recording a performance and not hand drawn automation so that may yield different results. The MW data ends up in the pattern rather than an automation lane in the playlist.
EDIT: OK I've run the test and I can reproduce the issue here but only with drawn automation clips. Automation recorded from my midi controller does not seem to have the same issue:
FL 120723-2.png
So when using an automation clip if I change presets while the project is playing then automation stops working unless I double click on the Stop button. Then everything resets so I think Marcin is right in his assessment. I'm going to test other plugins to see if the results are the same.
EDIT 2: Ok I just tried in Sylenth 1 and Spire (simply because they have on-GUI mod wheels that can be observed as they move along with the automation) and the issue does not occur. Even when changing presets the MW keeps moving along with the automation clip so I'm not sure what's going on...
Here's a test project:
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