The commands are copy&pasted just fine here. I see no particular reason why they shouldn't be copied, either. You'll need to provide more information on your environmen and what exactly you're doing.

Also, please verify that the "missing" note information is present when you paste the clipboard content into a text editor like Notepad. If you have some helper applicaton running that mangles the text clipboard, it could be one reason why those notes go missing, for example.

I have found that the information is present upon being pasted into a text editor. However, it is not copied back to OpenMPT. I did some more testing and found that, if I use the Select Channel command to copy only the information in channel 12, it is pasted with no problems. However, when I selected row 0 by clicking the 0 on the left side and copied it, pasting it into a blank pattern, only the information for channels 1-3 appears. Pasting the information into a text editor shows everything that was copied. Although I do not know why it would be useful or should behave any differently, I have attached a different file for you to try. The information of interest is in pattern 28.
Also, if it proves useful:
After opening Insaniquarium Suite.it:

1. Select and remove patterns 0-26.
2. Select and remove patterns 39-50.
3. Select and remove patterns 52-68.
   At this point, you should be left with a total of 13 patterns (specifically, patterns 27-38 and pattern 51).
4. Open the Cleanup dialog.
5. Check the following items:
   In the Patterns category:
   a. Remove unused
   b. Rearrange
   In the Samples category:
   a. Remove unused
   b. Rearrange
   In the Instruments category:
   Remove unused
   In the Plugins category:
   Remove unused
   In the Miscellaneous category:
   Remove unused channels
   Click OK and click Yes on the dialogs that appear.
   You should now have 13 patterns labeled 0-12. Copy the information in pattern 1 and paste it into a new pattern. You should try both selecting all information and selecting only row 0 to see if everything pastes as intended both times. You might want to use 2 blank patterns (one containing the entire contents of pattern 1 and the other containing the content of row 0 only). I used the Undo command after each paste operation. In theory, either method should produce the same results.
   Worst-case scenario: I need to copy all 13 patterns individually on a per-channel basis. That will take a while. But, if that is what needs to be done, that is what needs to be done.

Ah, I was testing with the latest stable version, this only occurs on tempo and speed commands in current test builds.

r17068 fixes this.