low and carbonation

I have noticed in my batches consistent low  and slow carbonation ; i have brewed 6 extract batches now..i use the standard bottle filler and fill to the top just running over and remove the filler  thinking that this is more or less the correct level after removing the filler ..i never really checked before but this only fills the bottle to about 1.5 " from the top not within  the  1" my recipes call for..could this be the reason for low and slow carbonation? eventually most of the bottles fully carbonate but it is usually like 6-8 weeks after bottling to become consistent..thanks for any help

#1 and #2 problems are improper amount of sugar added and storing at a temperature too low.  give them 2 weeks at a steady 70f and they will be fully carbonated if the other variables are correct.

i used the amount supplied by the store i bought the recipe from which was 5oz . this is  what i have received for  all  the 5 gal batches i have brewed.. thanks for the input..

I don't think a small amount of head space is going to make a difference.
What is the ABV percentages of your beers, how long have they been fermented/secondaried? These are some of the things that can affect carbonation times.
I've had one of my most memorable beers, a 10.5% Imperial Stout that took over 4 months to fully carbonate in the bottle. But once it did, it was a Super Beer.