Hey everyone,
This is my first time submitting a patch to an open source project, so please let me know if I am doing anything wrong.

The error was in output/cvs.c . When writing the column data (not headers) it started at channel 7 instead of 0. I verified this by comparing channel/sample data in gtkWave vs excel. 

--- old/cvs.c 2013-05-18 03:04:51.983610613 -0900
+++ new/cvs.c 2013-05-18 03:02:50.225777374 -0900
@@ -200,7 +200,7 @@
 
  for (i = 0; i <= length_in - ctx->unitsize; i += ctx->unitsize) {
  memcpy(&sample, data_in + i, ctx->unitsize);
- for (j = ctx->num_enabled_probes - 1; j >= 0; j--) {
+ for (j = 0; j <= ctx->num_enabled_probes - 1; j++) {
  g_string_append_printf(outstr, "%d%c",
  (int)((sample & (1 << j)) >> j),
  ctx->separator);