Hi Jowi,
Thanks for doing that testing. I'm of two minds, but will need to do some serious investigation. No way should a PHP function cause cpu stalls.
Either way, thankfully you've proved that the speed is the same unless you view the web gui. Unless you are refreshing the GUI for 8 hours straight you won't see a huge difference.
I'll need to review the code to inspect what changes might be causing this slowdown. Whatever it will be, IT IS NOT DANGEROUS. It will simply be something that causes I/O interruption, something that browsing a share while parity check is running will do as well.
Im having the a similar problem which i think is related to this.
I noticed this when doing reads of large files from shares.
Using the windows 8 file transfer graph, which is quite useful its easy to see the reads stop momentarily every 5 seconds for a short time before continuing,
This is also visible on the network throughput monitor