It is a long-standing, known issue (search using Google) that, as the game progresses (it is not clear exactly when, however at around day 30ish it happened to me), Morrowind/Tribunal/Bloodmoon will require multiple button presses or mouse clicks to, at least: jump, sheath/ready weapon, sheath/ready spell, activate hotkeys and cast spell/attack.

This happens only within 'inside' areas like houses and dungeons and is virtually game-breaking during the final Tribunal quest. I have experienced at most 8 separate keystrokes/clicks before a given action is taken and, on average, it requires 3 keystrokes/clicks to activate a given action ever 3-5 actions except casting spells/attacking -for some reason this is plagued by the issue less.

There is absolutely no workaround for this other than 'cheating', as the purported file cleaner (again, search using Google) works for some and not for others. This is also not an issue of button assignments, faulty hardware, or anything other than Bethesda's genuine lack of care in developing their games and listening to QA. Persistent players can continue to play through this issue but it should be noted that, all things considered, it will happen and it isn't anything that the player did to cause it.

Relevant Notes
1. I started a game of Morrowind with no expansions loaded, progressing in order and activating one expansion at a time as I beat it. The above issue was experienced in 'vanilla Morrowind' and persisted into Tribunal.

2. Particularly frustrating areas like Tribunal's Sotha Sil, Dome of Kasia can be navigated by 'cheating'. Players are advised to open the console ( ~ key by default) and type 'togglegodmode', all one word and all lower case, to effectively bypass the area. Opening the console again and re-typing the above code will turn god mode off.

I would like to add that this is not a general problem of Morrowind - but certainly very. annoying for those who are affected by it.
I myself have played Morrowind and its expansions for lots of hours (and far beyond day 30) without having had this issue once.

This is a very, very relevant point to make.

It is uncommon but, due to it occurring when and how it does, players affected by it are forced to cope with it or restart their games -potentially losing a bunch of hard-fought progress. (It's the sort of thing that simply should not happen and makes sense of the various issues Bethesda games have had on the PS3 as it's clear that they just don't check their code.) Simply put, even though it is not common it is the kind of thing that is very likely to put off players affected by it.