Compliments are often due to how a person sees the world - they compliment the things they notice or are impressed by.

Those things need not be real, just percieved - the complimentee who seems to be acting selflessly may have hidden motives (and I mean this as opposed to lacking the talent that may be complimented).

Compliments can be good for confidence - the complimentee may be uncertain or lacking confidence of their skills in an area.

Compliments can also be corrosive - Ego turning to Id, hidden weaknesses being overlooked and not worked upon until its too late.

As a peeople I would expect most adults get uncomfortable recieving compliments, though it may help some thrive.

I used to get uncomfortable with compliments because as You said id always be looking for their hidden agenda. Now I simply smiled and thanked the person. Then paid it no further thought. Its like saying 'well done' to someone. You take it on the chin and move on. It doesnt really need to be paraded up and down the street.

Im aware that I rarely give compliments. Because im aware just how big headed people can get. I once complimented a colleague on the suit she was wearing (shes normally dressed like a chav) and she went over board and thought I was hitting on her =/ ... so naturally i took it a step further and said 'Dinner and a Movie but you're paying' LOL. I was kidding ofcourse, but the look of her going absolutely red was priceless.

My fiance said the same thing. That i dont give compliments often either. I told her thats because when i do give them, I really do mean it and im not saying it to butter her up.
... im beginning to think i joke around too much.

"Engage Serious Mode"!

Just hold the compliment in your hand and throw it away. 

Think nothing of it.

I don't think much of compliments. I'm the sort that just say thanks and if they continuously keep saying what they think I go slightly red and embarrassed and jokingly say: Staaaap it.