I can't seem to reproduce this issue here. I use the following script to reset the toolbar to a default state, remove all separators, and then save to toolbar.ini.
test {
toolbar -r
var %n = 1
while (%n <= 9) {
toolbar -d sep $+ %n
inc %n
}
toolbar -fs
}
If I exit mIRC and then run it again, the toolbar loads correctly. Can you provide a minimal script, like the one above, that reproduces the issue for you?