C++ running inefficiently in Bash

C++ running inefficiently in Bash

I have a query regarding bash. I have been running some of my own C++
programs in conjunction with commercial programs and controlling their
interaction (via input and output files) through Bash scripting. I am
finding that if I run my c++ program alone in terminal it completes in
around 10–15 seconds, but when I run the same through the bash script it
can take up to 5 minutes to complete in each case.
I find using System Monitor that consistently 100% of one CPU is used when
I run the program directly in terminal whereas when I run it in bash (in a
loop) a maximum of 60% of CPU usage is recorded and seems to be linked to
the longer completion time (although the average CPU usage is higher over
the 4 processors).
This is quite frustrating as until recently this was not a problem.
An example of the code:
#!/usr/bin/bash
DIR="$1"
TRCKDIR=$DIR/TRCKRSLTS
STRUCTDIR=$DIR
SHRTTRCKDIR=$TRCKDIR/SHRT_TCK_FILES
VTAL=VTAL.png
VTAR=VTAR.png
NAL=$(find $STRUCTDIR | grep NAL)
NAR=$(find $STRUCTDIR | grep NAR)
AMYL=$(find $STRUCTDIR | grep AMYL)
AMYR=$(find $STRUCTDIR | grep AMYR)
TCKFLS=($(find $TRCKDIR -maxdepth 1 | grep .fls))
numTCKFLS=${#TCKFLS[@]}
for i in $(seq 0 $[numTCKFLS-1]); do
filenme=${TCKFLS[i]}
filenme=${filenme%.t*}
filenme=${filenme##*/}
if [[ "$filenme" == *VTAL* || "$filenme" == *VTA_L* ]]; then
STREAMLINE_CUTTER -MRT ${TCKFLS[i]} -ROI1 $VTAL -ROI2 $NAL
-op "$SHRTTRCKDIR"/"$filenme"_VTAL_NAL.fls
STREAMLINE_CUTTER -MRT ${TCKFLS[i]} -ROI1 $VTAL -ROI2 $AMYL
-op "$SHRTTRCKDIR"/"$filenme"_VTAL_AMYL.fls
fi
if [[ "$filenme" == *VTAR* || "$filenme" == *VTA_R* ]];then
STREAMLINE_CUTTER -MRT ${TCKFLS[i]} -ROI1 $VTAR -ROI2 $NAR
-op "$SHRTTRCKDIR"/"$filenme"_VTAR_NAR.fls
STREAMLINE_CUTTER -MRT ${TCKFLS[i]} -ROI1 $VTAR -ROI2 $AMYR
-op "$SHRTTRCKDIR"/"$filenme"_VTAR_AMYR.fls
fi
done