Messages stuck with green flag A. Status (XI 2.0)

Hi All,
  we are running an instance of XI 2.0 and for this interface in particular we are pulling a file off an FTP server via the file adapter and pushing it through to a remotely enabled function which creates a batch session on our SAP R/3 4.6C instance.  The interface used to work but we have now changed the name of the function within R/3 then made the corresponding changes in XI.  Since we've done this the messages appear to be getting caught up somewhere between XI and R/3.  The XI monitor (SXMB_MONI) shows in the A. Status field a green flag.  To me this would imply that it is processing on the remote end (R/3) however there has not been any batch session created.  This flag remains green indefinately.
  I thought it could have something to do with XI caching some old objects so I ran tx SXI_CACHE and did a complete cache refresh (F6).  This did not change anything.  I have cleared all messages out of the queue using tx SM58.  Then after reading another post in this forum I ran tx smq1 and smq2 to clear messages out of there but there was nothing in those queues.
  When I push another message through it will sit in SXMB_MONI with the A.Status field having a green flag.  Then I look in tx SM58 and find that the status text field displays "Transaction executing" for a very long time.  Eventually it changes to "timout during allocate of registered program / CP" but the message is not going through.  The only thing that has changed has been the name of the function in R/3.
any thoughts?

Hi Mark,
  under the 'Target System' column in transaction SM58 it says "AI_RFCADAPTER_JCOSERVER".  When I test it out it seems to work fine ... no errors.
When I looked at the trace labeled "Adapter_rfc.log" within the adapter engine it lists the following error.
>>RfcAdapter> Tue Oct 11 07:46:12 CDT 2005>>
> cannot load function template for Z_XI_INTERFACE_TEST1
> exception occurred, detail:
> com.sap.mw.jco.JCO$Exception: (104) RFC_ERROR_SYSTEM_FAILURE: CPIC-CALL: 'C
> MRCV'
I'm not sure why we get this error.  The function template Z_XI_INTERFACE_TEST1 does exist and we were using it before.  If I run the interface again this error will no longer appear.  It almost seems like it will display only once a day.
any other thoughts?

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