While perhaps not the same as the issue you are describing, it is not uncommon for HL7 messages to end up being double wrapped in MLLP envelopes. This is particularly if the message is transitioning through another system. (say from a billing system, through an EHR)
a standard envelope is
<VT>...hl7data...<FS><CR>
but a double wrapped message will look like this
<VT><VT>...hl7data...<FS><CR><FS><CR>
It's just something to look out for. And should be corrected by the system in the middle unwrapping and rewrapping the message correctly.