I used re-writable CD's to transfer files between my PC & Amiga for months, before investing in card readers for all my systems. Works fine, I'd dump files onto the CD's and read them back on my Amiga. 3.9 doesn't have the 8.3 filename limitations that some other Amiga CD-reading software has, but it would still bomb out occasionally if I had (for example) like a 100-character-long filename, lol. 
MakeCD is a horrible nightmare of a program that I wouldn't wish on my worst enemy, but it works. Wish someone would come out with better CD-writing software for Amiga's. 
Also, you say "both Boing Bags installed". You know there's 4 now, correct? The two unofficial ones add a lot of new features, def. recommend. 
Surprising, i find makecd works just fine and is relatively easy to use?
8+3 problems are nothing to do with amiga, thats ms/dos style limitations although ffs doesn't have really long filenames,they are still longer than 8+3 stuff-a good reason to always use pfs/sfs. no amiga cd software is stuck with 8+3.
There is also fryingpan(can do DVD also),masteriso,and burnit(never had luck with burnit).