No have not but the AV9107 and it gets its reference from the 14.318Mhz xtal. Possibly bad ? Have seen those need replaced before.....
added: maybe something first part in this can help pinpoint clock issues: Octek hippo vl+ 3.02 no POST no Beep no Code

yeah, there is a good chance something is off with the clockgen.

will verify that tonight.

Ok, the clockgen is fried.
Only frequency it outputs is 8MHz.

jumpers might be tired/stretched and not conducting

Have you tried putting a jumper on the turbo switch header or in the BIOS setting 'BOOT Up System Speed' to high?

Am sure you already checked but something to look at in 9107c datasheet: download/file.php?id=158842. Is the buffered clock out 14.318Mhz ok on pin 13 ?
And status of /PD pin 6 ? If pin 6 is grounded it puts the clock gen in power down mode if I read the pdf correct (page c-24). Yes maybe the Turbo switch shuts the clock off or on ??....

Spent some time on this problem today.

Everything is ok with the clock generator, but there are problems with the configuration jumpers, unless i am missing something obvious.

Combined picture of motherboard, clockgen frequency table + pins, some relationship lines and jumpers of interest.

JP28 and Jp29 are 3-pin jumpers, where pins 0 and 2 are connected to GND and pin 1 is +5V.

The frequency configuration table of the motherboard seems to be incorrect.
It states that jumpers 28 and 29 need to be either in 1-2 or 2-3 positions, but in both cases that will pull FS1 and FS2 down.
Jumpers must be removed entirely to pull FS1 and FS2 up.

Nothing appears to affect FS0 and FS3.
FS0 is set to 0 and FS3 is set to 1 at all times.
This is not good because i am interested in 40, 50, 66MHz frequencies which requires control over their state.

Was able to track FS0 to an inverter, but couldn't find where it goes from there.
Was not able to find connections to FS3.

Socketed the clockgen chip and simply bent FS0 and FS3 sideways to configure the desired frequency (default state of the control pins is HIGH).
Will probably add dedicated jumpers as a more elegant approach later, but for initial testing the above is practical solution.

Turbo switch has no effect.

At the same time i have never seen a BIOS with such options.
Quite different than the standard SIS, UMC stuff.
There are two options related to default speed and turbo, but they don't make any difference.

Ok and no I do not think Freq table wrong on quick inspection. Any speed with i after is internal not true clock gen output.
So a DX2-66 shows as same jumpers DX33 and DX100 which it should (ext clock 33mhz).
From the 9107-03 1995 pdf it shows this and would be what I assume the board was using.
All FS# shows pulled high internal on -03 so FS3 pulled high internal on -03 causing it to be 1 already so no jumper needed.
So grounding should change any FS# from 1 to 0 if I read it correctly. Below is what I think the board design was after but could be wrong. Not sure why FS0 has an inverter....
You should be able to get 40Mhz and 50Mhz direct clock if I read the design right....
Maybe your board has a ground issue or something else, I see lots of resistors just above the clock chip....
added: I also see how the clock gen can put out 8mhz. With FS3 auto pulled high=1, and there other FS# grounded 0 makes 8mhz...so maybe jumpering does not pull them high
Maybe the inverter off FS0 is bad ?

I had a system a couple of months back "go bananas" and I thought it was a crystal ref problem, turned out the turbo switch was glitchy, like breathe on it and it was randomly on-offonononoffoff.. so don't necessarily trust 35 year old case switches. Might be on when you think they are off and vice versa.

Another board I had back in the day was weird. The turbo setting in BIOS only had an effect when the turbo switch was strapped to on, and then the ctrl + or - worked too. I was trying to put it in a turbo button-less case at the time and it was really messing with my head until I stuck a jumper on the turbo header in desperation and it finally worked right. Just saying there's some weird ones out there. That one was a 386 with a 4.77ish turbo feature so it was a real plodder stuck on low.

Check my note about how the manual is misleading, or at list this very motherboard here does not behave that way.
Both pints 1 and 3 of jumpers 28 and 29 are GND, so no matter in which position you set them (1-2 or 2-3) the result is the same. The jumper cap itself must be removed to change state. This enables only 25 and 33 MHz frequencies since FS0 and FS3 are permanently set to 0 and 1, correspondingly.

And as bitwrangler said - TURBO switch does nothing on this board.

Sorry yes I read that and figured your board has a quirk not so much the manual. Odd that 28 and 29 are ground both ways, would think one way GND other is +5 or just NC (to allow the internal Pull up to work).
Sounds like your solution is the only easy one to gain the 40 and 50Mhz clocks back. Good work !