The only thing that will automatically disable muxes is my code that checks for invalid (un-tunable) ones. Note: un-tunable in this context does not mean an inability to receive the signal etc... It actually means the freq (or other params) are outside of the valid range for the tuner.
Check to see if you're getting any errors such as these in your logs:
Oct 19 07:48:11 [ERROR]:dvb: "/dev/dvb/adapter1" tuning to "99,999,980 kHz Vertical (Default (Port 0, Universal LNB))" -- Front configuration failed -- Invalid argument, frequency: 89399980
This is an invalid mux that gets auto detected on ASTRA-28.2 and so is rejected. If this rejection code is rejecting things it shouldn't then I'll take a look.
Adam