I checked with the same data as you posted and found no problems. I'm guessing that there may be a problem in at least one of the three files that is making them unreadable by our usual function possibly because of hidden formatting problems. Try using 1dcat on each of these three files to see if they are being interpreted properly; the row labels should show up as zeros, but the other values should show as you've written them. Also you may want to post the exact command you used. The command I used to test was this one:

1dSEM -theta testthetasliang.1D -C testcorrliang.1D -psi testpsiliang -nrand 100 -DF 5 -stop_cost 0.01