Which version of eCS? For v1.2MR or earlier, yes, for a boot drive, it is. You will need a 500GB (or smaller) drive, or to partition the drive with only a 500GB install partition. That has been resolved in eCS v2 (and possibly in older versions with updates). I put some pretty extensive details on this someplace in this forum... one of multiple threads related to it is here:
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http://www.os2world.com/forum/index.php/topic,1321.0.htmlOne would need (at least) the entire LVM 14.105 package to remove that limitation, which means updating the install disks with it, so one can install.
That aside, sounds like you have disk issues. I'd download Hitachi/IBM Drive Fitness Test (ISO), burn it to a CD, boot off it, then scan all disks using the Full/Advanced Scan. It's free and comes in very handy.