It's just a blind shot in the dark, but here's a possibility.
I took two minutes to look through the gsch2pcb.c code, which lives in
utils/src. There are a number of places where a 1024 byte character
buffer is created at the beginning of a function, like this:
add_elements(gchar *pcb_file)
{
FILE *f_in, *f_out;
PcbElement *el = NULL;
gchar *command, *p, *tmp_file, *s, buf[1024];
^^^^^^^^
You could try changing this magic number to 2048, say, at all places
in the file (there are 5 or six of them). Then rebuild & reinstall.
There are a number of magic numbers and paths hard-coded into
gsch2pcb. We have a lot of smart people working in improving gschem
and PCB. The link between the two, gsch2pcb, doesn't receive as
much attention, and seems to cause a number of problems. Maybe next
code sprint I'll take it upon myself to learn how it works and spend
some time polishing it. Or maybe somebody will beat me to it! ;-)