Investigating the Sourceforge CVS tree, I have found the offending
commit to be 1.135:

date: 2010/01/20 12:40:53;  author: robertl;  state: Exp;  lines: +4 -1
When writing routes, set class to map type instead of user so that duplicate 
waypoints aren't created.

$ cvs diff -r 1.134 -r 1.135 garmin.c
Index: garmin.c
===================================================================
RCS file: /cvsroot/gpsbabel/gpsbabel/garmin.c,v
retrieving revision 1.134
retrieving revision 1.135
diff -r1.134 -r1.135
772c772
<       way->wpt_class = 0;
---
>       way->wpt_class = 0;  // user waypoint by default.
968a969,971
>         // map class so unit doesn't duplicate routepoints as a waypoint.
>       rte->wpt_class = 0x80;  
> 

Reverting this change fixes the problem.

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https://bugs.launchpad.net/bugs/701600

Title:
  [regression] upload route to garmin, route truncated, no waypoints

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