I just found this today, and seeing there wasn’t anything else on it, here goes:

I have multiple computers in my apartment, and a few on a Linux machine being virtualized via VirtualBox, with a bridged network configuration.

I have a Hamachi gateway network through the same machine my VMs are being hosted on, and all non-virtualized machines can be seen from my remote machine through the gateway. The VMs cannot be seen through the VPN gateway.

Problem

VirtualBox bridged networking by default bridges to the main network adapter on the box when the machine is created. Typically, this is eth0. The problem is that when Hamachi sets up a gateway, it creates a shiny new bridged adapter on top of that- ham-br0 by default. VirtualBox is still talking only to physical eth0 adapter, so it can talk to everything except Hamachi.

Solution

To fix it, you need to make VirtualBox talk to Hamachi’s interface. This will not interfere with internal communications, either. Run the following command on the VM host while the VM in question is powered down:
VBoxManage modifyvm your_vm_name_here --bridgeadapter1 ham-br0