Perhaps sound examples of the sounds as they should sound and as they do
sound would be good for troubleshooting, to avoid some speculations.
Usually the method of elimination will lead to the solution.
Some speculations:
This happens even, if you play the Waldorf only, not live, but by a
sequencer?
- Issues could be caused by to much data for to less MIDI interfaces.
- Inaudible short latency and jitter, if you try to play the instrument
live, by this MIDI chain, e.g. you don't hear delay, but portamento is
sensitive to the way you play the synth, IOW even inaudible latency and
inaudible jitter, regarding to the time length, can become audible,
because the flow, how you play notes for filters that follow e.g.
portamento and legato, is different.
Another issue might be, that your masterkeyboard sends different types
of note off events, than the ALSA sequencer does send. Note off vs Note
on velocity 0.
I suspect something similar as the note off issue, perhaps after touch
vs enabled or filtered etc., or some MIDI data filter does filter
control data. Very common are filters that protect against to much pitch
wheel and modulation wheel data. Instead of 15 different controller
values during a 1/8 note, the software might send only 4 different
values. And again, it's very common to e.g. filter after touch messages
completely.
The MIDI connectors could also cause issues. You might use the same MIDI
cable, but you use different MIDI sockets.
Assumed you once used a "real" MIDI cable, where the male connectors
have thicker connector pins than a HiFi DIN connector has got and you
now connect to the female socket a male jack with thinner pins,
vibrations when playing the instrument on a wood flour could cause
unclean transmitted MIDI signals.
I can continue the speculations, as we say in Germany, "man hat schon
Pferde vor der Apotheke kotzen gesehen", Pferde können aber nicht
kotzen, IOW what's impossible by science, is possible in real live.
I e.g. experienced that the Roland MT-32's HiHat gets a bad timing, if
you play to many instruments, on different MIDI channels, with to much
data. If I play the same with the Yamaha TG33, also just one MIDI in,
there might be no issue for the HiHat. Such effects can be avoided, if a
sequencer has got no jitter and you minimal (1 or 2 ticks at a high
resolution) move some MIDI on events.
However, usually my experiences with MIDI (since MIDI was invented until
today) only lead to noise on Linux mailing lists ;).
Btw. are you sure that the Waldorf or anything else isn't broken and
it's just by random, that you experienced issues only, when you connect
to the PC and when you play some sounds? When building audio equipment
people I know and myself experienced "random" very often as something
that lead to astray.