To echo what's already been said, please don't format your entire post in code blocks. That should be used for code and program output. I'm sure many people have passed on helping because it was hard for them to read and understand the problem.

There seems to be a mismatch between your code segment and the example outputs. The first output says:

CCS: Fsize 216913920, pix 36152320
ETime=28.648 min, =97.60%, Event 'CCS: Extract RGB2C keys'
ETime=0.380 min, = 1.30%, Event 'CCS: Read_and_hash'
ETime=0.325 min, = 1.11%, Event 'CCS: Write_RGBC'
97.60% -> CCS: Extract RGB2C keys
 1.30% -> CCS: Read_and_hash
 1.11% -> CCS: Write_RGBC
Elapsed time = 29.58 min
[download]

But the time_event() calls in the snippet are:

&time_event('CCS: Counting RGB hash keys', \%e2at...
&time_event('CCS: Extract RGB2C keys', \%e2at,...     
&time_event('CCS: >open Output file', \%e2at,     
&time_event('CCS: Write_RGBC', \%e2at,...     
&time_event('CCS: Close_RGBC', \%e2at, $debug*0);
printf("CCS: %d bytes written to fn '$ofile'\n", -s $ofile);
[download]

But most of these do not appear in your output. It's also not entirely clear from the code how time_event() works. I could see some possibilities of its functioning that would mean you're measuring the reading time from the file, when you think you're measuring the call to keys.