This question has been asked quite a time ago, but seems like the issue hasn't been resolved. I'm running the MS Mouse and Keyboard Center on W8.1 64bit and I have the same problem. I googled and didn't find any solution, however I found a workaround:
On the overview where your macros are listed and for every macro, there are 4 icons on the right hand side (edit, copy, folder, delete). Click on the folder and it will show you the folder where the macros are stored. The macros are stored in XML format, simple enough to understand for most of us.
Lets tackle this with an example: assume you want to have a macro that does: Alt+Shift+F (automatic code formating in Netbeans). Using the MS Mouse and Keyboard Center, you will be facing the issue that you can't make the software understand that you want to hold the Alt-key like the Shift-key. But you will do as follows to get your desired macro:
1) Chose Alt from the special key listing below the editor, it will display Alt (10ms).
2) holt Shift and type F. Resulting in this sequence: Alt (10ms) (10ms) Shift(hold) (10ms) F(10ms) (10ms) Shift(release)
3) go back to the macros overview list and click on the folder icon to the right of your macro you just created (hope you gave it a meaningful name)
4) open the file with a
text editor like notepad, not word alike (word processors will probably mess with the formatting and break your file). You will see:
<?xml version="1.0" encoding="UTF-8"?><Macro>
<KeyBoardEvent Down="true">56</KeyBoardEvent>
<DelayEvent>10</DelayEvent>
<KeyBoardEvent Down="false">56</KeyBoardEvent>
<DelayEvent>10</DelayEvent>
<KeyBoardEvent Down="true">42</KeyBoardEvent>
<DelayEvent>10</DelayEvent>
<KeyBoardEvent Down="true">33</KeyBoardEvent>
<DelayEvent>10</DelayEvent>
<KeyBoardEvent Down="false">33</KeyBoardEvent>
<DelayEvent>10</DelayEvent>
<KeyBoardEvent Down="false">42</KeyBoardEvent>
</Macro>
5) now you cut out the 3rd and 4th line:
<DelayEvent>10</DelayEvent>
<KeyBoardEvent Down="false">56</KeyBoardEvent>
and paste it before the </Macro> closing tag. Resulting in this XML listing:
<?xml version="1.0" encoding="UTF-8"?><Macro>
<KeyBoardEvent Down="true">56</KeyBoardEvent>
<DelayEvent>10</DelayEvent>
<KeyBoardEvent Down="true">42</KeyBoardEvent>
<DelayEvent>10</DelayEvent>
<KeyBoardEvent Down="true">33</KeyBoardEvent>
<DelayEvent>10</DelayEvent>
<KeyBoardEvent Down="false">33</KeyBoardEvent>
<DelayEvent>10</DelayEvent>
<KeyBoardEvent Down="false">42</KeyBoardEvent>
<DelayEvent>10</DelayEvent>
<KeyBoardEvent Down="false">56</KeyBoardEvent>
</Macro>
6) save the edited content to the original file. Close the MK Center or click on another existing makro and go right back to the overview. This will reload the macros from file.
7) on the overview click edit to see the makro we just changed: We see the Alt-key is now pressed and released at the end of the macro. The graphical macro representation is correct.
8) go to Netbeans, or whatever software you create that macro for and try it out, it should work. With a bit of common sense, you should be able to adapt my example to your scenario and your macro.
I hope I could help someone with the same issue. Now you kids go and play your games with your fancy macros, I have to get back to coding

.