I solved the issue under Paul's support. I just post the final results
about this issue solving.
Despite the fact that on OSX new hypoinverse works fine, linux version
has some issue.
The reason: makefile.unix (for hyp2000_mgr on linux systems)
dependencies are NOT completely corrected so that if you do not do a
make clean, bad things result.
Now if do perform make for hyp2000_mgr after make clean - all is OK.
Command set:
cd ../src/seismic_processing/hyp2000_mgr
make -f makefile.unix clean
make -f makefile.unix
Please keep it in mind is if you use trunk version.
As Paul promises the makefile will be fixed before the release.
Andrey Stepnov