Usually it is pretty easy and efficient. However your molecule sounds like something really hindered and organic. Your trouble can comes from steric effect or from solubility. I suppose you are using piperidine/DMF. There are articles reporting alternative bases and solvents. You can try other reported bases (specially organic and non-bulky) and solvents or a little harder conditions if that does not affect your molecule.
I actually used piperidine / DCM 50%. But i dont think it works for me. Do you think using DMF will change? also if i use that system do you have any suggestions for the work up?
Man, I think it is just to try. I was not work with an similar structure to that one you describe, so I think it is hard to recommend an specific one. But another solvent or another base maybe could work. Try to find what other options people report on literature. Maybe an stronger or less bulky base. Hopefully you can do it. If not, maybe you can try a less bulky protection group, as well.
Removing of Fmoc by conventional bases might be problematic in your case. I had a similar experience with solution phase Fmoc-deprotection and I moved to conceptually alternative ways. In my case I used Pd/C-catalitic hydrogenation for Fmoc-deprotection. The reaction was somewhat slow but worked clear.
I have cleaved the Fmoc with diethylamine and precipitated the peptide by pouring it into ether or ether hexanes. You usually triturate the precipitate several times to get rid of the fulvene. Your compound may be a bit greasy so you may have some solubility in the ether/hexanes wash. I think the procedure is in this paper J.Med.Chem. 1996;39:1361-1371.
We worked with Fmoc-Glycine derivatives that were substituted by Tritylhydroxylamine at the carboxy group. We´ve used DBU (1.5 - 2 eq) in THF. The turnover is quite fast. We just evaporated the volatiles and purified the residue by flash-chromatography.