Cards with IBM RGB5xx RAMDACs use several different input frequencies for the clock synthesizer which can't be probed without some knowledge of the text mode clocks (which may be a wrong assumption if you're using non-standard text modes). Here is the procedure you should use to find out the input frequency:
First run
X -probeonly >& outfile
and check the output for the probed clock chip which might look like this:
(--) S3: Using IBM RGB52x programmable clock (MCLK 66.000 MHz)
(--) S3: with refclock 16.000 MHz (probed 15.952 & 16.041)
^^^^^^ ^^^^^^^^^^^^^^^^^^^^^^
there will be a "good guessed" value which will be used and two probed values in brackets based on the 25MHz and 28MHz text clocks. This probing can only work if you run a normal 80x25 or 80x28 text mode!
The refclock values known so far are:
STB Velocity 64 24 Mhz
Genoa VideoBlitz II AV 50 MHz
Hercules S3 964 50 MHz
Hercules S3 968 16 MHz
#9 Motion 771 16 MHz
depending on the quartz on your card and maybe other features like an additional clock chip on the Genoa card (which as a 14.3MHz quartz).
If you claim that your card has a 16MHz clock, but it really uses 50MHz, all pixel clocks will be tripled and a 640x480 mode with 25MHz will use a 75MHz pixel clock, so be very careful.
If you found the right refclock, you should set it in the config file (device section) e.g. with
s3RefClk 16
s3RefClk 50
so that that this value will be used even if you use another text mode and probing fails!