I've asked my eye doctor a bunch of questions (happens to be my ex-girlfriend's aunt) According to her, eye sight is pretty much genetics. Some people have great vision, some people, not so much.
I started starring at a screen in 92 but I was fitted for glasses in 91. I've worn contacts since 98 and 99.99% of the time and my vision has stayed a pretty consistent -3, -3.25 (in contact lenses) since.
Some stuff I've learned (about contacts):
If you get contacts that last 2 weeks - use new ones in 2 weeks - It sucks - Accuview (the brand I use) are pretty expensive (something like $300-400 for a year supply) but old contacts definitely cause eye strain. I generally change mine every 3-4 weeks.
Focus on something in the distance every once in a while. A benefit of being a smoker (if there is such a thing) is every couple hours I... go out for a smoke. Nice 5-10 minute break from starring at the screen.
If you don't have plans after work and go home and get back to work on freelance or a side project, or whatever - switch to glasses - glasses allow the eyes to breath and help rehydrate them.
Drink water! Eyes need water like the rest of the body.
Try something like Gunnar Optics maybe? http://www.gunnars.com/ I have a pair and wear them (with contacts) when my eyes are really tired. They help and according to the eye doctor, anything that can reduce eye strain is good.
Change your contact solution. I was using Renu solution for a long time then switched to bausch and lomb biotrue and my eyes have felt fresher since.
Wear sunglasses! With a UV filter preferably, but anything helps. People give me shit cause I wear sunglasses when it's cloudy but when it's cloudy is actually worse then when it's sunny. The clouds trap UV rays and that kind of weather can be more harmful to your eyes (and skin) then when it's sunny out.
If they continue to bother you, have your doctor re-test your eyes or put you in a different contact / lens brand. People are so quick to goto a medical doctor for problems, but often neglect going to an eye doctor or dentist. Sucks - most insurances don't cover eye or dental, but it is important to get those things checked out.