If I remember correctly, there is a bug in issues.alfresco.com about the webclient.properties file needing to be in a certain path "alfresco/extension". Also - another issue - , if you upload a file in the datadictionary, which exists with the same name in the alfresco classpath, the uploaded file is ignored.
maybe thats the same with your system. check issues.alfresco.com, which bug is your bug. either "vote" for the bugs to get them fixed faster - or open up a new issue, post the link here and the issue number e.g. [AE-1234] in the subject head of this thread