I had a similar problem with an ET200S CPU. On the first machine it works fine, but when I went to transfer the code to another machine, the clocks did not toggle. I tried Compile (rebuild all) and Download all blocks, but neither of these worked. Finally I did the following with good results:
1. Disable the clock memory
2. Download code version with clock memory disabled
3. Re-enable clock memory
4. Download code version with clock memory re-enabled.
In my case the bug in the TIA Portal is that once you set the clock enable bit, it assumes it is already set in the next download without checking the actual hardware. By disabling the bit, the software is convinced it needs to download the clock enable information. This should have been done automatically when I did the Download (all blocks) option.