The reason this happens is because Mechguns specifically, for whatever reason, fire the bullets from where the sprite for the gun is loaded rather than from the character. Normally your actual weapon isn't loaded, so if you're using mechguns and you aren't actually holding them the bullets will fire from coordinate 0,0 on whatever map you're currently on. That doesn't work for Falz (most of the time.)
The game can only load 12 pieces of visible equipment at a time. So, to fix it, you have to remove one of the visible sabers in your stack (the first 12 that you equipped) and then equip the weapon you actually want to use. If you can see your gun, you've done it corrrectly.
You can actually do this at the very beginning of the run without losing a saber. Equip the leftover saber from the stacking glitch, then remove one of the first 12 stacked sabers (easiest being the one in slot 2.) Then equip your handgun or rifle and they should be visible when you get down onto Ragol.
It's also worth mentioning that refreshing your mag can temporarily mess this up. If you re-equip your mag and it de-equips your weapon because you no longer have enough ATA (usually early in Ruins with a Shot) the Mag will actually take up the visible sprite slot. If you can see your mag, you know that's what happened. You can easily fix that by just de-equipping the Mag and equipping a weapon that you meet the ATA requirement for without it, THEN re-equipping the Mag.
Hopefully that covers all the bases. Let me know if you need clarification on anything.
I agree that some degree of pausing should be allowed for longer categories, but I struggle with where to actually draw the line. As a general goal, I'd like to keep the IGT and RTA as close as possible. The further apart they get, the more it becomes like a segmented run. The quality of play from someone who will do a 20~ hour IGT run in say, 23 hours vs doing it in 40 hours will likely be hugely different. That's still not the same as an actually optimized segmented run for sure, but it starts to lose the feeling of an RTA run when the amount of actual time that has passed is twice the amount of time you actually spent playing the game. If setting an arbitrary limit of RTA vs IGT and then using the IGT is just the simplest answer, then so be it, but I'm not sure what that threshold should be set at. 2x seems a bit high. Also, all of it would still have to be recorded and having almost half the run being a break seems a tad ridiculous.
I don't have any experience doing really long runs as I can barely do 4 hour categories, so I am unsure on what would constitute a "reasonable" amount of breaks for something that will take most of if not an entire 24 hours. There's also the matter of whether it should be a limited number of set length breaks, or a pool of time to be drawn from + used at whatever points the runner needs. A limited number of set length breaks would be easier to enforce, but might put runners in a more difficult position if they suddenly need to get up and leave for just a few minutes.
Assuming we're including breaks but staying in the spirit of an RTA run, I think that breaks should be included in the recording. We should have a designated spot for players to take a break. I'd personally suggest character selection, with the character currently being played selected + info displayed so the IGT is visible while the character idle animation spins and runs.
A second timer to indicate break length would be advisable, but that feels like something we should only address after we've come to a conclusion about how much time can actually be used for breaks.
I really don't know what to do in terms of permissible breaks that still keep the feel of an RTA run. If anybody has an idea of how much time they think would be beneficial, be that from experience or what you feel would personally work for you, please do share.
... Also, I wouldn't be opposed to adding a Segmented section specifically for All Difficulties Glitchless that simply uses IGT as the primary timing method and does not need to record anything but the actual gameplay, but that feels like a separate matter.
The closest category to that would be 25% which is both Episodes, All missions and the Soul Eater + Akiko's Frying Pan sub-quests. Basically it's normal mode 100%.
There are no Episode 2 quests at all in Offline mode, unless you have PSO+ (which are just a couple of pre-downloaded quests from Online) so there's no real need to include Episode 2 in an "All Missions" run.
Adding ID is pretty meaningless. The class thing is a welcome change, but at the moment the default view of the leaderboard (at least for me) only shows runs currently marked as RAcast, which is a little odd.