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Sounds like a TERM behavior. Which $TERM does it think you are using?

.profile is in $HOME ( ~ ).

Try something like 'export TERM=vt100 ; tset -Q'.

Your initial input is different than this one.
Following shouild work:
awk -F\" '/Cell id/{if(!a[$2]) cnt++;a[$2]++;next}END{print cnt}' gen_cell_orig_001.dsx

several problems
1. pass variables into gawk/awk with -v
2. print $0 > somefilename leaves the file descrptor open, if the file has thousands of lines with unique values you have thousands of...

I didn't go into your script very deep, but isn't this line missing slash at the beginning?diffdir="var/local/dsx/diff"
diffdir="/var/local/dsx/diff"

Defining some variables
Calling a script or binary named dsxdiff with various options and writing stdout (1>) in one file and stderr (2>) into another file
grep in a file for a pattern and if...

filename=${cfile%%.*}.dsx
mv $cfile $dsxdir/${filename##*/}

sorry...

filename=${csvfile%.*}

and loose the quotes around *_bsc_*

Another well known approach

$> file="/var/local/dsx/import/gen_cell_orig_001.dsx"; echo $(basename "$file")
gen_cell_orig_001.dsx

$ echo "/var/local/dsx/import/gen_cell_orig_001.dsx"| cut -d '/' -f6
gen_cell_orig_001.dsx

Have a read of:

Learning the Korn Shell, 2nd Edition: Chapter 4: Basic Shell Programming (http://oreilly.com/catalog/korn2/chapter/ch04.html#ksh2-ch-4-sect-5.3)

or:

Manipulating Strings...