Mann_B, the first question to ask is "Is your process I/O-BOUND or CPU-BOUND?" If you do not know this, do not attempt anything else since you are just as likely to have no impact or make things worse rather than better.
If the process is I/O-BOUND, then changing the initialization -- even reducing the intiialziation time to zero -- will have NO IMPACT upon the program. An I/O-BOUND program is waiting for I/O to complete, and reducing CPU usage will not affect that program (unless the I/O is impacted).
Only if the program is CPU-BOUND can changing initialization possibly have any impact. AND there will be an impact if -- and only if -- the initialization is part of the code that is CPU-BOUND. If the initialization code is not part of the CPU-BOUND code, then again you could reduce the initialization time to zero and not have any material impact on how long the program runs.
In other words, unless you've done a LOT more research than you have shown so far in your posts, the results you are seeing would be expected. Changing random parts of a program to improve performance is a futile exercise. And code is not always predictable -- I had a development manager some years ago that was 100% convinced we needed to buy faster disk drives because the program was I/O-BOUND. I got access to STROBE and ran the program through it -- and discovered the program was heavily CPU-BOUND. We spent a week making changes to the appropriate section of code and cut the overall elapsed time by 80%, which saved about 4 hours a day. If we had bought faster disk drive, they would not have improved the program's run time one percent -- and they cost a lot of money!