as of March 9, '07 skillups in the SQ Mage Tower still worked fine for me, but it's a truly mind-numbing pain in the back. I started training in the mage tower from about 110 skill level, every 5-10 levels I would go in and train up. Start with the lowest porter, blue, and just get in a rhythm. After a skill of 200 or so I switched to the red porter which will allow you to go all the way up to max level. I was up to about 300 when the new changes took effect but have still trained up to 345 since then. I think the higher your skill level the longer it takes for a skillup to occur, by 340 it just took forever, like the other person stated, a full 15 minutes of constant rotating for maybe 1 skillup, but sometime a quick 1 or 2 in a row.
Compared to swimming or harvesting the safefall was the worst skill to "train". I'm not going to bother with the last 5 skill points for me, the time was too insane and I really don't jump/fall much, with the adornment which reduces falling damage by 35% I feel covered for most/all mistakes I might make. Like someone said, it helps to have a regen totem active while training so the damage you take won't cause you to stop for too long before the next jump. I can jump off of the highest level, yellow, and only take around 3k damage, about half the time I take no damage at all.