I found the origin of the problem when installing on master (instead of slave) 
hdd. 
There is a Host Protected Area on the disk with a size of 1 Mb. When image is 
being deployed  boel kernel says that there is a HPA and the it says that it 
was disabled.
When system is booting scientific linux, it’s kernel does not disable this 
area, so disk becomes truncated. Consequently, the last partition is out of 
disk. 
If drive is in slave mode, than kernel does not detect HPA at all ☹ in both 
kernels. 

The solution is quite simple (but still rather difficult to google it ☺ ) – you 
should pass ‘hda=stroke’ option to the kernel  - than it also ignores HPA on 
the disk.
Of you you can simply rewrite autoinstall script to think that disk size is 1 
Mb smaller, or 10Mb. 

I suppose it is a bug in systemimager, because different kernels are used 
during system installation and system operation. This causes bad things like 
above, and there could be other problems of this type.

Despite this problem systemimager works great.

Thanks to all.


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