So, I'm currently playing with AFT enabled, none of my other mods *ought* to alter follower behaviour, although, you know, who knows sometimes. I've used AFT for ages with no problems (other than it possibly messing up someting with INPCs, but I've not used that lately) and I haven't added any new mods since starting this character yesterday. I had Meeko pretty much from the start, had no problems. Bought a horse in Riften, had no problems. Headed to Riverwood and befriended Faendal, problems start. Nothing enormous, but unnerving and suggestive of Worse To Come.
First, more or less as soon as Faendal joined me (which, AFAIK even in vanilla you can have a human + a dog follower?) Meeko refused to follow for quite a while, went through dismissing/re-enlisting a few times, nothing helped, luckily reloading a slightly earlier save seemed to bypass whatever the issue was. So, fine, okay.
Second thing, I take advantage of AFT's default setting of followers not dying if they run in front of your sodding bow, yet after finishing off the last bandit in Embershard I wander up the path to loot the swine and find... Faendal's body. Don't think I even hit him, although maybe I did, but anyway, he's somehow died even though he should be immortal. I must admit I was lazy and console resurrected him rather than reloading, but I'm sure I've done that before with no issues (pre-AFT follower immortality). Guy seems fine, so, okay, head back to Riverwood (where I, erm, get an inheritance letter as apparently my dear friend Faendal has died...) and tell Faendal it's time to part ways as I'm off to Whiterun for the night. Look around to check Meeko's following and Faendal hops on my horse! Re-enlist him and make him stand away from the horse, part ways again, he gets right back in the saddle. (Eventually I made him stand way further from the horse and sprinted to it when I dismissed him, which worked).
Anyway, TL;DR version, followers are being odd, help!
I've asterisked the most recently-added mods, the Fine Goods from Morrowind one is a little glitchy appearance wise but I've been playing with even the new ones for a few days (I play quite a lot because Reasons) although I guess I didn't have much in the way of followers in that time. I'm not massively attached to this character, although I'd like to get to the goal I've set for her (own a house based mainly on doing 'mundane' work type stuff rather than going round looting stuff - Embershard being the exception because I have to do it to get Lakeview) but if I have to restart, I'll cope.
Unofficial Skyrim Patch.
Unofficial Dawnguard Patch
Unofficial Hearthfire Patch
Unofficial Dragonborn Patch.
fine goods from morrowind. *
Character Creation Overhaul.
CCO SkyRe Patch.
fine goods from morrowind_gray quarter *
CCO - Oblivion Carry Weights.
CCO - Permanent Birthsigns.
Guard Dialogue Overhaul.
Drinking Fountains of Skyrim.
CCO - Dynamic Skill Progression.
acquisitive soul gems.
Sit Anywhere. *
Reduced Distance NPC Greetings. *
AmazingFollowerTweaks. (re-added a few days ago after a period of not using it)
mjhKhajiitSpeakDLC - Dawnguard.
mjhKhajiitSpeakDLC - Hearthfire.
mjhKhajiitSpeakDLC - Dragonborn
mjhKhajiitSpeakMod - Localized Thieves Guild Jobs.
mjhKhajiitSpeakMod - NPC Bartering
mjhKhajiitSpeakMod - Realistic Needs And Diseases.
CCO - Diverse Races And Genders