Hi Juan,
I don't have adjtimex in my system.
I thought it was a base system utility. Maybe you don't care, since it seems that you are close to finding the real problem. You can go to ftp://mirror.switch.ch/mirror/fedora/linux/core/2/i386/os/Fedora/RPMS/ and get the adjtimex RPM. Make sure that the above directory is the right one for your system before installing.
[root@kalimotxo log]# hdparm /dev/hdc
/dev/hdc: multcount = 16 (on) IO_support = 0 (default 16-bit) unmaskirq = 0 (off) using_dma = 0 (off) keepsettings = 0 (off) readonly = 0 (off) readahead = 256 (on) geometry = 16383/255/63, sectors = 234441648, start = 0
It appears that the disk driver fell back into 'dumb' mode for some reason. Run your older kernel and see if it shows using_dma = 1. If so, it is highly likely that this is the source of your ticks loss.
Sorry, I know nothing about IDE. (I only answered your original post because it seemed like an NTP problem.) If you can't find the answer in the archives or with Google, try posting another question about IDE DMA not working.
--Stewart
