Hi @tiromos
I have double checked calculation procedure manually, and it seems that calculations are OK. Sorry for misleading you.
When in the code formula

the following values are used
k - reduction factor for lateral buckling (0.5) like in your model 2
L - length of the element (6000 mm) like in your model 2.
C1 =0.97 - due to k<=0.95 as described in my first answer
calculated value of Mcr = 1.64 kN*m (as in Robot)
So what is the reason for difference between model 1 and 2
Using reduction factor 0.5 for lateral buckling length, does not simulate intermediate bracing (as expected in your case) but rather full lateral buckling restrains at beam both ends. Code formula is constructed for single member with lateral braces defined on member ends.

Such formula construction causes significant difference in Mcr calculation when different k and L values are used regardless constant (k*L) value.
In your model 2 Robot calculates results for k=0.5 and L=6000 mm while you expect results for k=1 and L=3000.
In your model 1 Robot calculates results for k=1 and L=3000 mm (as you expect) In both cases (k*L)=3000.
It is possible in Robot to use k=1 and L=3000 for continuous member with length 6000 mm (Model 2), when intermediate bracings are used, or reduction coefficient will be define for Lz member calculation length. Refer to my previous post or the following article. I would recommend using inermediate bracings for such simulations.
Once again sorry for misleading you in my previous post.

Krzysztof Wasik