Centos – Konsole works, gnome-terminal doesn’t

I'm running on CentOS 5.7 (in case that matters) I have a program (not my own) that runs fine from Lonsole, but when I run it from xterm, gnome-terminal or rxvt, it just hangs.

I'm doing this with a completely fresh account, no .bashrc, no alterations to defaults. Brand new vanilla install.

On both terminals, $- is himBH so, both the same type of shell, I would think.

If I ssh into the machine, even from itself (ssh 127.0.0.1), it works in all terminals.

Any idea what could be wrong?

EDIT: The program is qconf, part of SGE (GridEngine), in case that matters. It goes to a server and returns a list of machines that are allowed to make compute requests.

I ran with traces, the diff looks like:

diff broken working
1,4c1,4
< execve("/opt/SGE/bin/lx24-amd64/qconf", ["qconf", "-ss"], [/* 49 vars */]) = 0
< brk(0)                                  = 0x1a48c000
< mmap(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x2ba0bec8a000
< mmap(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x2ba0bec8b000
---
> execve("/opt/SGE/bin/lx24-amd64/qconf", ["qconf", "-ss"], [/* 48 vars */]) = 0
> brk(0)                                  = 0xa7cb000
> mmap(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) =     0x2b3b4716e000
> mmap(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x2b3b4716f000
6,19d5

.
.
.
< futex(0x3a408030ec, FUTEX_WAKE_PRIVATE, 2147483647) = 0
< futex(0x6ba3c0, FUTEX_WAIT_PRIVATE, 2, NULL
\ No newline at end of file
---
> open("/proc/cpuinfo", O_RDONLY)         = 3
> read(3, "p", 1)                         = 1
> read(3, "r", 1)                         = 1

[working goes on from here]

Broken stops in mid futex output, which is odd.