Hi,
can you post your LTspice file, or relevant section of it?
Initially I was thinking that the probes in x10 mode wouldn't allow the generator to match impedance correctly, but after that thought percolated for a bit, it didn't really make sense in relation as to how a FRA setup needs to be implemented.
The chapter 19 in the MSO5k user manual doesn't give much info about exactly how to connect the generator to the circuit under test, with the 'tips' picture showing a coupling transformer to impress the sweep signal on the test circuit. Just a suggestion of some type of pulse transformer, but I've also seen power amp modules for inclusion into bode measurement setups.
Some vids on FRA implementation by cleverscope give a reasonable overview.
This is a feature I'm trying to get more familiar with on my testbench.