You could manually set the hotkey ID's (the 4 character field). Then (with version 1.5) you can click the ID column header to cause the list to be sorted by the ID's. Just make sure you don't duplicate any (or HotKeys will change it without you noticing) and if you use "Execute Multiple Commands", be sure to change the ID's there as well.
For example, make all your text commands have ID's such as txt0, txt1, txt2; programs could be prg0, prg1, prg2; internet could be net0, net1, net2; etc. Good luck!