I'm just wondering how you go about finding mod conflicts.
For example, I came to the realisation the other day that it had been a long time since I'd seen a giant. I thought nothing of it at the time.

Then I did a bounty quest where I was to go and kill a giant. Searched around the location for hours and couldn't find it. The marker was jumping around all over the place - I thought the giant had glitched through the ground or something. Eventually I used TAI to turn off the Ai and followed the marker to an Elk. Upon killing it, it told me that I had killed a giant, and to collect the bounty from the relevant hold.

This process has repeated once since that time, with a deer.

Anyone got any hints as to find which mod is causing this problem (or alternatively, have had this problem themselves without mods)

Was it a really big elk?

Well that sounds like its an issue that involves spawns and leveled lists. Best way would to go through and read all the readmes for any mod that might modify creatures(Giants count as creatures) or spawn points. Im using neither types of mods, besides PISE, so I havnt experienced that issue myself. Then deactivate about half of them, rest for 3 days, and see what happens.

You could post a list of mods your using though.

Hahaha I thought so I could see that coming along. It was called "Elkmale"

Mod list. Firstly Mods that are most likely to have an impact

Adventurers and Travelers
DovahSka
Giant Dragons
Ring of Sputnik

Spend Dragon Shouts for Perks
Statue Invasion in Markarth
Master And Expert Hoods
Added Rank to Enchanting Extra Effect
Ask Follower Skills
Stones of Barenziah Quest Markers

Fixed by removing Wars in Skyrim : Dark Rainbow (which didn't make it onto earlier list due to an oversight on my behalf)