An overlay software (in the veins of EZ-Drive or Ontrack Disk Manager) translates the C/H/S geometry for systems that do not support the size of the HDD (or the substitute).
That is only necessary if the older system in question does not support that HDD size, which could be the culprit of the copied files sometimes being readable and sometimes not.
The fact that you can boot from it, but are not always able to read the copied files tells us that the older machine at least detects the CF card as (some, maybe wrong) type of HDD. But it seems to have a problem with the partition (either its size, file system, etc.). Which could mean you are passing an "unsupported barrier". This could very well be fixed, if applicable BIOS HDD type settings can be manually set. If not, one could fall back to using overlay software.
That being said, it could very well also be a faulty card or adapter, as derSammler mentioned.
What are the older machine in question's specs?