I've set up a chroot system to automatically build the latest versions of software. I just made a mirror copy of my root file system and removed unneeded packages for this setup. Then I do chroot /mnt3/buildfs and proceed to build Qt4 and kde4 as root. After it completes successfully, I can run the programs in the chroot, but once I copy them outside to where I want them (same relative prefix), running them hangs the computer (I suspect a deadlock because some programs can never finish after you run one of those qt4 programs).

Does anyone have any idea what's causing this?

Run the program under strace. This will show you where it is getting stuck and may help identify the deadlock.

I'm pretty sure I've found the problem. I recompiled kde4 without being in a chroot and the problem still happens. Obviously, user programs should never crash the system - so there must be something wrong with the OS (which in this case is most likely the C runtime library - I'm using glibc 2.7 which probably has compatibility issues. I also remember cinelerra having problem when it uses glibc 2.7. Guess I'll have to wait until they fix these regressions.

Here's the tail of strace

read(3, 0x66fd00, 2048) = -1 EAGAIN (Resource temporarily unavailable)
brk(0x69f000) = 0x69f000
brk(0x697000) = 0x697000
writev(3, [{"l\1\0\1\24\0\0\0\6\0\0\0\177\0\0\0\1\1o\0\25\0\0\0/org"..., 144}, {"\17\0\0\0org.kde.dolphin\0", 20}], 2) = 164
poll([{fd=3, events=POLLIN, revents=POLLIN}], 1, 25000) = 1
read(3, "l\2\1\1\t\0\0\0\7\0\0\0=\0\0\0\6\1s\0\4\0\0\0:1.3\0\0\0"..., 2048) = 89
read(3, 0x66fd00, 2048) = -1 EAGAIN (Resource temporarily unavailable)
writev(3, [{"l\1\0\1\0\0\0\0\7\0\0\0{\0\0\0\1\1o\0\20\0\0\0/MainApp"..., 144}, {"", 0}], 2) = 144
poll(

[{fd=3, events=POLLIN}], 1, 25000) = 0
poll([{fd=3, events=POLLIN}], 1, 0) = 0
poll([{fd=3, events=POLLIN}], 1, 0) = 0
poll([{fd=3, events=POLLIN}], 1, 0) = 0
poll([{fd=3, events=POLLIN}], 1, 0) = 0
poll([{fd=3, events=POLLIN}], 1, 0) = 0
poll([{fd=3, events=POLLIN}], 1, 0) = 0
poll([{fd=3, events=POLLIN}], 1, 0) = 0
write(2, "<unknown program name>(2241)/: C"..., 371<unknown program name>(2241)/: Communication problem with "dolphin" , it probably crashed.
Error message was: "org.freedesktop.DBus.Error.NoReply" : " "Did not receive a reply. Possible causes include: the remote application did not send a reply, the message bus security policy blocked the reply, the reply timeout expired, or the network connection was broken." "

) = 371
exit_group(255) = ?
Process 2241 detached