I cannot reproduce that here, so more precise reproduction steps are necessary. To be sure, do you mean that you change the transpose values in the sample tab, or are you transposing the sample map of the instrument? The latter isn't possible in XM / XI, so e.g. C-5 will always map to C-5.

Yes, in the sample tab. Here is the instrument i was seeing this problem with currently, the "hisser 5" sample is always transposed to F#4 when I am saving as F4.

I marked reproducibility as "sometimes" because there are some instruments where i always have this problem every single time, but with other instruments i never run into it.

Which module format are you working in while working with the instrument?

I think I found the issue now; this is a variant of a bug that was fixed a while ago when converting MPTM/IT/S3M to XM, but it wasn't fixed when saving an XI file from within an IT/MPTM module. This only affects samples with a middle-C frequency below 8363 Hz. I'll provide a fix shortly.

Should be fixed in r14687 (+ backport for OpenMPT 1.29 in r14688), available in an hour or two at https://builds.openmpt.org/builds/