ghost files and time machine . . .

PLEASE FORGIVE MY EXCESSIVE DETAIL, BUT MY MAC-TECH SAYS YOU'LL NEED ALL THIS . . .
the byte count on two identical files has changed and this happened after i installed time machine and rockstor in march. these files are memoir ONE and memoir COPY. i am very good about dupping a chapter on mONE over to mCOPY if i rewrite or edit in the memoir. before time machine and rocktor i did not have this problem. i was saving to a shuffle [pack of gum] and a kingston flash drive and the count was always identical. but since april 29th there is a difference of around 4000 bytes. ONE [on which i always do the work] has the lower count. it makes me very nervous. i check the count of the whole file whenever i complete work on a chapter. i have checked ALL chapters in both memoir files and they are identical, but the count for the whole file is different. EXAMPLE: mONE is presently at 1,654,377 and mCOPY is at 1,657,449. a day ago, they were 1,654,522 and 1,657,594, respectively. [i did very little editing between these two days.] i've been to Mac Authority in louisville and was told there's probably "ghost files" at work, here. it very confusing. as i said this problem only surfaced AFTER i got time machine and rockstor. i am up-to-date and running leopard on my Macbook Pro. i have no 3rd party connections. my configuration is by insight broadband [cable].