Yes, the way I used to give the pickups is quite buggy indeed. I don't like much the standard way either because it has some bugs relative to certain gametypes and pawns.
But either ways, all the mutators are being built from scratch, differently from the "standard way", but also different from my old way.
For instance, I have already finished in Nali Weapons 3 what I call a "dynamic swap mutator", which basically permits to replace all the pickups, ammo and weapons correctly in a map, in such a way that:
1) "loaded" works flawlessly;
2) You can replace 1 weapon by many different ones, as the mutator is NOT bound by 1 weapon = 1 replacement, but 1 weapon = some different replacements (good to replace the redeemer by a set of different nuclear weapons for example);
3) It can also be used to make the replacement from total different packs (it's universal and independent);
4) The regular replacement mutators always had problems in replacing the SkaarjTropper weapons, well, not anymore (they get replaced perfectly and the skaarj can use them without any problem at all);
5) Certain bugs like "shooting ammo" in certain weapons are fixed with this new different aproach;
6) You can choose to either replace a class of weapons, or its entire subclass;
7) Also another feature is that you can just completelly remove something from the game rather than replacing it (by setting the new item to "X").
Also, I am thinking to make a mod menu for this mutator (so it can be tweaked there instead of on the ini, although the difficulty is quite the same - it's really easy to change stuff there).
The new mutator has much less code, is better organized and has much more stability, but again, it doesn't use exactly the "standard aproach" the mutators normally use on replacements, as it has a few really annoying bugs.
So don't worry, the new version will have that fixed and enhanced, so pickups won't stay around on spectators and such