The first issue is that it adds duplicate tables for the company, which is taking that much more space on our server and is just annoying when we are doing SQL reports. We also had an issue with our views disappearing, but I suspect that was an issue with the installation.
The other annoyance is the added steps of publishing any security changes when we only have one company. It takes about 2 minutes longer to make a small security change because it has to publish between the two companies.
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