I have firmware rev. 25, which I believe is current so no need to downgrade.  I think what you are experiencing is a side effect of the way the firmware interacts with the driver.  Are you using Jack? Personally, I use VLC with jack so I can play audio files while I have Harrison MixBus open.

Remember that when you change samplerates in windows, the number of channels available in the hdsp mixer changes. In order to play back 88.2/96k (2x) sample rates, you must force the ALSA drivers in Linux to change the available mixer channels as well. 

Try this:

1) open the alsa terminal mixer by opening a terminal and typing alsamixer

2) make sure that the madi card is the master clock source (I'm trying to find a way to make this work from an outboard clock source, but I haven't had time to fiddle with it)

3) change the internal sample rate to whatever samplerate you want to play back

4) try to play back your file

Note that if you are using Jack, you must also change the samplerate in the jack gui before starting Jack.

Following these steps, you should be able to play back whatever sample rate you want.  The trick is just to use ALSA to trigger the format change just like you must trigger a format change from the hdsp settings window from windows.  I NEVER use anything beyond 96k since I think it's pretty much just marketing hype anyway so I havent tested my process with those rates, but for me, 88.2/96k work great as long as I use alsamixer to set the rate before playing my song or starting Jack. 

Also note that if you are not using Jack, you DO NOT necessarily need to do this when switching frim 44.1 to 48, or from 88.2 to 96 because it's the 1x, 2x, 4x state that you are changing not specifically setting the samplerate. 

Sorry if this is confusing, it's hard to explain simply.  Please reply if you have more questions.  I'll do my best.

Peace,
Brian