Motherboards will only accept the biggest one in slot 1, and the smaller one in slot 2.
That's no true. Unless the mobo specifically states otherwise it should be able to use the RAM no matter the slot and/or size.
check yer manual, some mobo's require you to put RAM sticks in certain slots...to boot up correctly...
like 1 and 3
and 2 and 4
sometimes that is the problem
Generally thats just for dual channel use, not just booting up in general.
What brand are the two sticks and what are their specs? Meaning how fast they are and what timings they are running.
If you can boot using each stick individually then use CPU-Z to get the info with each stick regarding brand name, stock MHz and timings.