Sreccvt (and of course its GUI) is useless when it comes to converting nonpaged addresses $8000-$BFFF. You say that PPAGE is set to 3D. But sreccvt doesn't know that $8000-$BFFF belong to page 3D and there's no way to tell sreccvt where to move $8000-$BFFF to.
To solve the issue you could exlude 8000-bfff from your "linear" memory map. But this is probably not what you want. So you need to extract 8000-BFFF S-records to separate file and shift these to proper "page" using sreccvt with -of switch. For example to move 8000-bfff to page 3C use -of switch argument set to (page=3C * 0x4000 - 0x8000):
sreccvt -m 8000 FFFFF 32 -of E8000 -o sfile8000bfff_OUT sfile8000bfff_IN
Then you should put sfile8000bfff_out back into your S-file. This converted S-file will be compatible with sreccvt and its GUI :smileyhappy:.
grep may help moving 8000-bfff to separat file.