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This is more a heads-up than a bug report. I've heard that the maintainer of hwclock has ported some patches from clock which fixes Jensen bugs. Recently you've put together a clock-1.1-7 package (which works on the Jensen). Please let the hwclock maintainer know about the recent fixes so that hwclock can be kept in sync. Maybe you can get rid of clock forever once hwclock has all the bells and whistles. This would streamline the init scripts a little too.
Hmm... if you change line 327 (or so) of the latest util-linux from: cmos_write(10, (save_freq_select | 0x70)); to cmos_write(10, (save_freq_select | clock_ctl_addr)); does the util-linux hwclock then work for you?
Actually, in this case you want the 0x70 because this is used as a bitmask...not a clock address! This was the same bug fixed in the Jensen patch to the clock. It should always be 0x70 regardless of the Alpha platform it's running on.
The hwclock in Bill's util-linux-2.9w works fine on all the Alpha's I tested on, including Jensen. I think this one can be relegated to "NEXTRELEASE". :-)
Fixed in util-linux-2.9w-26, initscripts-4.59, timeconfig-3.0.2-1.