Why does matrix selection behave differently when using which?

Dear R community,

I have a medium sized matrix stored in variable "t" and a simple function "
countRows" (see below) to count the number of rows in which a selected
column "C" matches a given value. If I count all rows matching all pairwise
distinct values in the column "C" and sum these counts up, I get the number
or rows of "t". If I delete the "which" calls from function "countRows" the
resulting sum of matching row numbers is much greater than the number of
rows in "t".

The table "t" I use can be downloaded from here:
https://github.com/groupschoof/PhyloFun/archive/test_selector.zip
Unzip the file and read in the table "t" using t <- read.table("test.tbl")

The above function "sumRows" is defined as follows:
sumRows <- function( tbl, ps ) {
 sum(
   sapply(ps,
     function(x) {
       t <- if ( is.na(x) ) {
         tbl[ which( is.na(tbl[ , "Domain.Architecture.Distance" ]) ), ,
drop=F]
       } else {
         tbl[ which( tbl[ , "Domain.Architecture.Distance" ] == x ), ,
drop=F]
       }
       nrow(t)
     }
   )
 )
}