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[VGMArchive]

I have FST files from a game Aleshar.  I'm trying to create FLACs from these for archival/historical purposes.  I tried Foobar2000 to play them back but couldn't (OpenMPT installed).  I tried XMPlay and it does play it back (OpenMPT installed).  However, there's a few obscure behaviors:
- From a single song of length 6:09 (according to XMplay's playlist), it generates 3 output FLACs.  I put them together using Audacity and they seem to match up.  Why is it splitting them? 
- The third file has an abrupt stop of the module.  As best I can tell, the song does not repeat anywhere.  It seems like it's stopped rendering the song to FLAC at 5:57.

Is there a better way to render these FST files to FLAC (or even WAV)?

Also, I'm doing the same for the MOD archive.  I run into various problems there too so this might help there as well.....

[Saga Musix]

I downloaded those files from ModLand and they play just fine in OpenMPT. So whatever issue you are having with them in foobar2000 is not directly related to OpenMPT. It could be due to the file extension (not sure how the foobar plugin exactly handles the format detection), so you could rename them to .mod and see if that helps them being recognized in foobar2000.

Why is it splitting them?

Because it's not just one single tune, but each of those files contains multiple subsongs. You can see this information in the General info tab in XMPlay, where it tells you how long each subsong is. In OpenMPT you can see the same information using Player -> Estimate Song Length.

- The third file has an abrupt stop of the module.  As best I can tell, the song does not repeat anywhere.  It seems like it's stopped rendering the song to FLAC at 5:57.

Those songs are supposed to loop indefinitely, as the subsong information in XMPlay will show you. MOD files do not contain loop metadata, so XMPlay offers several options to configure how files should be looped (e.g. how many times), if they should be faded out after the loop, etc.. Go to the options window and then to the Miscellaneous section, where you can change all the relevant settings.

Is there a better way to render these FST files to FLAC (or even WAV)?

XMPlay is great for batch conversion of modules.

Slightly off-topic:

I'm trying to create FLACs from these for archival/historical purposes

I'm a bit puzzled by this. The best way to archive those files is to leave them in their original format. If you want them to be easily accessible online, you build a module player based on libopenmpt (e.g. using Cowbell or chiptune2.js). A FLAC file recorded with anything but the original tracker isn't really historically accurate, since many players will not play each file 100% like the original tracker does. While such playback bugs may get fixed in later versions of that player, it means that you have to keep re-exporting FLAC files every time such a playback bug is fixed. Hence I'd either go with archiving recordings from original hardware (like the SOAMC project), or just directly provide the original module files.