> Setting HZ back to 100 fixed the problem.
>
>   Is this some bug in HTB or HZ has to be set to 100?

ehh other thought - htb is tested with HZ=1024 or HZ=100.
You said that you use HZ 1000.
In include/net/pkt_sched.h:
#if HZ == 100
#define PSCHED_JSCALE 13
#elif HZ == 1024
#define PSCHED_JSCALE 10
#else
#define PSCHED_JSCALE 0
#endif

I'm not sure if variable-HZ patch repaired this too. Simply
QoS subsystem is not aware what to do with this HZ rate.
You might try to redefine PSCHED_JSCALE to be 10 for your
case.
Also try to set PSCHED_CLOCK_SOURCE to PSCHED_CPU in the same
file. It might help.
devik

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