When you execute a KeyQuencer macro from a HyperTalk or AppleScript script in a HyperCard stack, the rest of the script doesn't wait for the KeyQuencer Macro to complete. I have written a KQRunning XFCN that checks whether KeyQuencer is still working, but using it in a wait loop can lock up HyperCard if you're not careful. The problem lies in the fact that HyperCard doesn't respond to menu commands or mouse clicks when it's running a script (either HyperTalk or AppleScript), so that KeyQuencer macros will wait forever if they are targeted to HyperCard itself. The wait loop is fine if you're driving other applications from HyperCard via KeyQuencer, but you'll have to use a different method to drive HyperCard itself.
One possible solution is as follows: have your HyperCard script end with the call to KeyQuencer, and have the KeyQuencer macro end with a call to a second HyperCard script that takes over where the first one ended. As an example, the KeyQuencer macro could call this second macro by clicking on a button with the "Click" command.