My team has answered the following problem many times, it seems to be a very common mistake. The problem is that the account that the biztalk host is running under (usually BtsInstanceHost) does not have enough permissions on the directories acting as the send/receive locations for the file adapter. The fix is to grant the Biztalk host account “Full access“ to those folders (modify might not be enough for some strange reason)
I recommend having one directory (i.e. d:\BtsFileEndPoints) that contains all file send/recieve locations. That way you can configure the permissions once, and never have to worry about it again.
Event Type: Error
Event Source: BizTalk Server 2004
Event Category: BizTalk Server 2004
Event ID: 5644
Date: <date>
Time: <time>
User: N/A
Computer: <computer name>
Description:
The Messaging Engine failed to add a receive URL "ReceiveLoc1" to the adapter "FILE". Reason: "File transport does not have read/write privileges for receive location 'C:\PickUp\'. ".