This line works:

  set %spotline %callsign %county1 $+ , %state1 %freq %mode

whereas this line does not:

  var %spotline %callsign %county1 $+ , %state1 %freq %mode

When using "var" instead of "set" the I get %callsign and %county1 in %spotline, but I don't get any of the rest of the line:

  10-12-2011 14:57 GMT - AD1C Erie

If I only change "var" to "set", I get it all:

  10-12-2011 14:57 GMT - AD1C Erie, NY 7056.5 CW

Any idea what's up with that?

This is because /var and /set doesn't share the same syntax:

var %spotline %callsign %county1 $+ , %state1 %freq %mode
A quick workaround is to use the -l switch on /set to make a local variable using the /set syntax

As Wims pointed out, commas are used in /var to separate multiple variables on the same line. You can use /set -l as he mentioned, or you can replace the comma with $chr(44).

var %spotline %callsign %county1 $+ $chr(44) %state1 %freq %mode

Thanks!

If you need variables to be referred to after your script has finished its routine at a later time, setting global variables are recommended over the local ones. The local variables are set temporarily and unset when a script has completed its task.