I have 1,000 research an hour. And recently i have noticed that i have been short research points. And no i have not been hacked

How much has it been? The 1000 is rounded, so if you're short by less than 1 per hour it's probably because of that.

It depends, sometimes i will get 1,000 because i have exactly 1,000 but if i already have 1,000 sitting i will lose like 2 or 3 points

since this is directly related to your account and you feel it's not the rounding error causing the problem, you'll have to contact Dan directly so he can look at your account and see what's going on...

see instructions here: viewtopic.php?f=5&t=583

You might want to visit EACH of the planets that you own as well to ensure the production counter is correct. Planets don't auto-update their production when they increase their development during the first five days after you colonise/invade it. Visiting a planet updates the counter for you, but you have to do it for every planet you own and will ever own.

im guessing your actual is 999.75
So rounding it up (as i imagine the game does if .5 or over) it would appear as 1000
but after 4 incomes you would lose out on 1 research point as the math would finally come round and add up
This is just an idea anyway, im not sure. your best asking dan.

Fixed, i had to visit a planet i conquered