I just tested the attached zipped .exe under Windows XP with a byteblaster II cable (no FPGA attached though). It still works:
$ ./jtag_tester
Test application for JTAG chains
=====================================
Select JTAG interface:
=======================
1. Altera ByteBlaster
2. Cypress UltraISR
Enter option: 1
Windows NT/2000 version: 5.1.2600 (A280105)
ByteBlaster detected ok.
ByteBlaster enabled ok.
Test options:
=============
1. Toggle TCK
2. Toggle TMS
3. Toggle TDI/TDO
4. Check JTAG chain.
5. Count the number of devices.
6. Read out the device IDCODEs.
7. Exit.
Enter option: 6
Reading device IDCODEs:
11111111111111111111111111111111 <no device>
<hit enter to continue>
You can use this program to toggle pins, read ID codes, etc.
Perhaps it'll help debug your issue.
I'd recommend first probing the TCK signals at each device and closely looking at the rising edges. If there is not a clean rising-edge due to transmission line reflections, then it will cause problems.
Cheers,
Dave