The rating used in any given tournament is usually your last published rating, which may not match your current rating. That rating is created on the 3rd Wednesday of the month and becomes active on the 1st day of the following month.
Some tournaments may use your current rating, or some other rating based on specific cut-off dates, but that should be mentioned in pre-tournament publicity.
So, a tournament in January would use the rating you had as of the 3rd Wednesday of December 2013. Looking at your rating history, it looks like you were paired under the correct ratings based on your official published rating for those months. One thing to note, this particular process used to be a little different and your current rating and published ratings had a longer lag time; that changed in September of last year.
I don't know why, but once around Januaray 2012 I lost badly in Empire City Open (from 1133 to 1108). The reason behind it was because they put my rating from Fall 2011, which was 1212. And in that tournament 1200 rated players belong to the U1800.
Later I participated it again (Empire City 32nd annual) and did well, however my rating still dropped from 1108 to 1099 because I won 3 times against low rated players (below 1000) and lost twice against 1200's.
My latest tournament I joined was a nearly a month ago in Brooklyn Marriott, strangely my rating was supposed to be 1098 but the USCF tournament directors put it at 1108, which was my old rating from 2012 Empire City Open (NOT ANNUAL). Can someone answer this, because I'm rather confused that USCF don't keep track of my ratings.
THANK YOU!