Hi Stefan,
Issue #1: Usually I have updated my Segger firmware with the Segger updater utility which is as well provided with the Segger files inside KDS (C:\Freescale\KDS_1.1.0\segger\JlinkConfig.exe). Running that utility allows you to update the firmware too. Interestingly that it works with the 'Flash from file' functionality in KDS, obviously this has not built in that timeout. So thanks for that tip!
Issue #2:
You can select an individual Segger unit. For this you need to know the USB identification or serial number. You can use the JLinkConfig.exe mentioned above:

You get that number reported in the Console view of Eclipse too:

Now all what you need is to pass this number with the -select command (see below):

The C:\Freescale\KDS_1.1.0\segger\Doc\Manuals\UM08001_JLink.pdf explains that option (and others).
I hope the helps,
Erich