In the Config\Shares folder on the flash drive, there's a .CFG file for each of your shares.
It will have a shareInclude=<...> line and a shareExclude=<...> line that will list all of the included and excluded disks. You should NOT set both of these manually ... you set one; then UnRAID simply lists all of the other disks on the opposing list. I don't know what happens if you set them manually, and the intersection of the two sets isn't exactly the complete set of disks.
But, for example, your Files.CFG should have these three lines in it (among others):
shareInclude=disk3,disk4
shareExclude=disk1,disk2
shareAllocator=highwater
I removed the excludes from the settings page like you suggested. The config file now reads:
shareInclude="disk3,disk4"
shareExclude=""
shareUseCache="no"
shareAllocator="highwater"
shareSplitLevel="999"
So it seems the settings are being written correctly. Not sure what the deal is