This blog post is now obsolete since version 2 of the owncloud client now supports multiple accounts.
Thanks for all positive responses!!!!

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As for accessing multiple owncloud instances on one pc.

I am running 2 Owncloud clients next to each other succesfully on a Windows 7 system.
There are several ways to do that, the essence is running the software with different users.
Those user accounts allready have to exist, in this example i’m using User-A (my main user) and User-B (a separate owncloud user)

First method is by using the task scheduler

Create a task that runs owncloud.exe when you logon.
Select: “run whether the user is logged on or not” and select the user that has to run that task (in this case User-B).
As a trigger select “at log on” and select a specific user: “yourpc\User-A” (your main account)
As action, point to owncloud.exe (probably “C:\Program Files (x86)\ownCloud\owncloud.exe”)
When hitting OK, you’ll be asked to type the password for User-B
Now run the task. You’ll be asked to set serveradress, uername password and folder for owncloud data.
Do not use the same folder as your first owncloud instance.
That will seriously screw up your data.
After rebooting you’ll see 2 processes. Only 1 interacts with your desktop.
Data will now be exchanged with 2 different owncloud systems.

Second method is by using psexec

psexec:
http://technet.microsoft.com/en-us/sysinternals/bb897553.aspx

Place the psexec.exe somewhere in a folder. Create a batchfile in the same folder “start-second-owncloud.cmd”
Put the line into the script that starts owncloud using psexec:
psexec -u -p -d -i “
in my example:
psexec -u User-B -p p@ssw0rd -d -i “C:\Program Files (x86)\ownCloud\owncloud.exe”
if you don’t wanna place a password in a script, which i can imagine, just leave out the password entry.
psexec -u -d -i “
you’ll be asked the password for User-B everytime you’ll be starting the script when you log on.

Start the script using task scheduler or just place a shortcut in your startmenu-startup folder.

Now when logging on you’ll see 2 owncloud icons in your tray.
Both can be managed seperately and interactively.
Do not point multiple instances to the same folder.
That’ll screw up your data.
You can copy data from 1 owncloud folder to another, no problem.

The first method mentioned above i use to run owncloud on servers regardless of people that are logged on, to synchronise local scripts.

I’m using the second option without the password option on my pc’s to connect to multiple owncloud servers.
Works like a charm.

Good luck!