A quick point, you are using 2 eq of triethylamine and 10 eq TMSCl. Are you taking further precautions in the workup to keep the pH up? If you don't add any more base, aqueous workup will generate alot of HCl unchecked, and this may be causing your TMS groups to fall off.
I would personally use an excess of triethylamine over TMSCl, or actually just run the reaction in neat pyridine.
If deprotection is a problem you could also use a more robust silyl group, like TBDMS.
As far as the column goes try, as macman104 suggested, EA/HEX systems where hexane is the major component. If that's still too polar you could use ether instead of EA as your strong solvent.