I had that same problem in a jetta i had.  What was wrong was the sensor in
the coolant resevior.  It was malfunctioning telling me their was low
coolant when their wasn't.  The part was about 25 dollars and cake to
install.  I havent looked at my syncro to see if it has the same sensor but
it would be a good start for you,
Adrian

>From: Evelyn Mitchell <efm@TUMMY.COM>
>Reply-To: Evelyn Mitchell <efm@TUMMY.COM>
>To: vanagon@GERRY.VANAGON.COM
>Subject: Coolant LED flash 87 Vanagon GL Synchro
>Date: Tue, 11 Jan 2000 18:36:20 -0700
>
>During highway driving, the LED in the coolant temperature indicator
>periodically flashes (1-5 times). The guage reads in the middle of
>the range, to a wee bit high.
>
>What might be the cause of this? A failed LED? A real overheating
>problem? Temp seems to be normal, but...
>
>Evelyn Mitchell
>efm@tummy.com
>
>--
>http://www.tummy.com/ Consulting and Software for Linux and Unix
>KRUD - Kevin's Red Hat Uber Distribution - the Freshest Red Hat every month

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