The "count" key gives you the message number in a given file whereas "countTotal" gives the message number in a set of files. The former gets reset for every input file on the command line but the latter keeps on increasing.
Here is an example:

% grib_count -v file1 file2
     1 file1
     5 file2
     6 total
% grib_ls -p count,countTotal,shortName file1 file2
file1
count       countTotal  shortName
1           1           t
1 of 1 messages in file1

file2
1           2           msl
2           3           tcc
3           4           tcw
4           5           str
5           6           2t
5 of 5 messages in file2

6 of 6 total messages in 2 files

So the count for the 1st message of the 2nd file is 1 (reset) but countTotal is 2.