The password (if saved by user) is stored in the sqlyog.ini file on local machine. So this is not server related. It must be a de-obfuscationg failure when we read the file. As you experience this wiht specific servers it may be an issue with specific connection names.
Best of all was if you could send the sqlyog.ini file to us when it appears. Don't attach here but create a private ticket. And yes .. we will be able to connect and even reverse engineer the passwords. But we need such testcase. However maybe details for a single [connection] section in the file will be enough.