Raflex, I think what you might be observing is that the PLC does not turn it's outputs on immediately, and the inevitable delays between writing the strobe pulse into the tag database, and it being transferred to the output card become more significant at the higher speeds.
If you are doing all of your code in the cyclic task, there will be a variable delay due to the scan cycle, and there will be a variable delay due to the RPI update time of the tag being transferred to the output module.
You should be trying to reduce this inherant delay as much as possible in your application.
Consider using a either a fast Periodic Task, or, better still, an Event Task, to detect the counting input, and at counter .DN fire your strobe output tag.
EDIT: Event Task triggering from the HSC is not available in CompactLogix, therefore you will have to use a fast Periodic Task. You will have to determine how fast this needs to be.
Then program an IOT to the output mudule if the counter .dn bit is on. This will send the output data to the output module immediately.