Sorry for the late reply, but I was out of town for work and have just today gotten back to fooling around with this. 
Anyways, I tried your tips, changed a few things here and there, and well, it still doesn't work. So I started over, this time less complicated with only two characters and a new HKN mapping.
This is the macro I use on both characters:
Code:
/stopmacro [nomod]
/target [mod:ctrl,nomod:alt,nomod:shift,target=Beregond][nomod:alt,nomod:ctrl,mod:shift,target=Zillaya]
/follow
This is the HKN mapping:
Code:
//================================================================
//-----------------------------------------------------------
// DEFINE MAIL LABELS FOR SENDING KEY STROKES.
//-----------------------------------------------------------
<Label w1 Local SendWinM wow1>
<Label w2 Local SendWinM wow2>
//-----------------------------------------------------------
// FTL setup
//-----------------------------------------------------------
// %1% : Master Key
// %2% : Slave Key
// %3% : Modifier
// %4% : SlavesToSend
<Template SendMasterAndSlave>
<SendFocusWin>
<Key %1%>
<Sendlabel %4%>
<Key %3% %2%>
<EndTemplate>
// %1% : master key
// %2% : slave key
// %3% : modifier
// %4% : Active window
// %5% : Slave Windows
<Template SendLeaderless>
<If ActiveWinIs %4%>
<ApplyTemplate SendMasterAndSlave "%1%" "%2%" "%3%" "%5%">
<EndTemplate>
// %1% : master-key
// %2% : slave-key
<Template FTL>
<Hotkey %1%>
<ApplyTemplate SendLeaderless "%1%" "%2%" "LCtrl" wow1 "w2">
<ApplyTemplate SendLeaderless "%1%" "%2%" "LShift" wow2 "w1">
<EndTemplate>
//-----------------------------------------------------------
// NEW STUFF
//-----------------------------------------------------------
<ApplyTemplate FTL "F10" "F10">
<Hotkey Space>
<SendLabel w1,w2>
<Key %Trigger%>
The macro is bound to hotkey F10 in both WoW clients, and I unmapped the old key of course.
The first instance wow1 is the character named Beregond, wow2 is Zillaya.
Now the really strange part:
The script DOES work when wow2/Zillaya is the active window and I press F10. In this case, I have wow1/Beregond follow me instantly. However, it does not work the other way around. If I press F10 with wow1/Beregond being the active window, nothing happens. This really is weird! 
This is the output I get in HKN when I press the hotkey:
When I press F10 on wow1/Beregond I get this:
Code:
From this pc: <SendFocusWin><Key F10><SendWinM wow2><Key LCtrl F10>
<SendFocusWin> completed
<Key F10> completed
<SendWinM wow2> completed: Window found. Target set to 0x701E2 "wow2"
<Key LCtrl F10> completed
When I press f10 on wow2/Zillaya:
Code:
From this pc: <SendFocusWin><Key F10><SendWinM wow1><Key LShift F10>
<SendFocusWin> completed
<Key F10> completed
<SendWinM wow1> completed: Window found. Target set to 0x3028A "wow1"
<Key LShift F10> completed
I tried adding the <Wait 100> as suggested, but it did not change anything of the outcome at all. Any more ideas of what I can try?
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