root nameserver problems ?

Can I assume that the fact that www.microsoft.com no longer exists in the
DNS is a result of the (ongoing) root nameserver problems?

No.

Things have been really flaky since the INTERNIC/ALTERNIC flap the other day.

Indeed, but not the way you think.

daneel:8> dig www.microsoft.com @e.root-server.net

you are asking a nonrecursive server for data it doesn't have.

; <<>> DiG 2.2 <<>> www.microsoft.com @e.root-server.net
; Bad server: e.root-server.net -- using default server and timer opts

in fact you are asking a nonexistent server, so it used your default one.

[gw.home:i386] dig @a.root-servers.net microsoft.com ns | grep IN
;; microsoft.com, type = NS, class = IN
microsoft.com. 2D IN NS DNS1.microsoft.com.
microsoft.com. 2D IN NS DNS3.NWNET.NET.
microsoft.com. 2D IN NS DNS4.NWNET.NET.
microsoft.com. 2D IN NS ATBD.microsoft.com.
DNS1.microsoft.com. 2D IN A 131.107.1.240
DNS3.NWNET.NET. 2D IN A 192.220.250.7
DNS4.NWNET.NET. 2D IN A 192.220.251.7
ATBD.microsoft.com. 2D IN A 131.107.1.7