I'm having a similar problem.
I haven't backed up my USB bleepbloop in two years and god knows where the laptop with the original software is. So I've been using GBcartflasher, and when I transfer the .gb and .sav, VBA loses it and does this:
The tracks are empty and when I try to load anything it's empty. LSDJ manager gives me this:
Which I assume is nothing; I've never used it. What's up with this? The tracks work fine in console.
[*SOLVED*] UCP is what I needed, GBCF doesn't work in this instance. It's a wonder what a bit of searching warrants.
For anyone who has this exact problem: http://www.mediafire.com/?5jk69m4unlr59p5