I mean when you asked (since I don't use .ans myself--just added it for the convenience of others like yourself), just to be absolutely certain I simply downloaded ANSI version from the REXPaint website, unzipped it, quickly drew some glyphs on the default image and hit Ctrl-a to export, which displays the message "Exported images/unnamed.ans," indicating where the file was exported to. Open up REXPaint's /images/ directory and there's the .ans file as expected...
So first of all, I guess you'd have to list your steps and how they and the results are different from what I described above. I would recommend doing the exact steps I just mentioned, rather than working with whatever copy/version you're using right now. In a general sense, troubleshooting is about simplifying a process down to its most basic roots then gradually adding on extra complexities while checking to make sure everything's still working as expected with each addition. One of the things you're doing differently is affecting the results.
so i guess you can imagine how painful and tedious was making them on these tools, and how more comfortable would be making them on RexPaint! 
(and imagine also how many people will love to use RexPaint on .ans submissions there! ) )
For me I definitely prefer REXPaint workflow, but as one might expect, people used to those older tools actually still like them. Funny thing that just yesterday I saw someone mention that they love the extra features of REXPaint, but would prefer it have the workflow from PabloDraw since it's what they are familiar with xD
Nice work, btw, and I can imagine at least the first one would be much quicker to do in REXPaint by comparison
