I am looking if anyone has had any issues with customers using credit line checks being processed by a merchant that converts to ACH or refusal to take this type of check.

They are not eligible for conversion if labled a a draw on a credit account and a merchant can refuse any form of payment they want to.

If your bank doesn't label them as credit card drafts (and many banks don't) the only other way to keep them from being converted is to issue them as business-style (larger size) checks with a serial number encoded to the left of the FRABA number (in the so-called auxiliary on-us field). Such checks are ineligible for conversion and state-of-the-art POS capture devices won't accept them for ACH conversion.