Intracellular staining for cell suspension is very useful technique for flow cytometry research. However, the morphological change; the background signals are always the two major problems encountered. Commercial fix and perm kits sometimes work sometimes don't. In order to get a satisfied results, different antigen system might need different intracellular staining protocol.

Does anyone have experience in this area?

I don't have experience personally. But know that many immunologists or transplant immunologists are using this technique for the detection of cytokines. May be you should try those section to enter your question in order to get a better response.

Production, specificity, and functionality of monoclonal antibodies to specific peptidemajor histocompatibility complex class II complexes formed by processing of exogenous protein.
Zhong G, e Sousa CR, Germain RN.
Proc Natl Acad Sci U S A. 1997 Dec 9; 94(25): 13856-13861.


maybe?

You should optimise fixation/permeabilisation for each antigen you're staining for. paraformaldehyde/triton works well as a starting point but alcohol based fixation can also be useful

You must optimize fixation/retention conditions depending on particular antigen studied - for e.g. staining cytokines requires addition of monensin or brefeldin A prior to fixation, whereas many "CD" -protein subunits do not. Also, for other cellular mateerial such as DNA, the citrate based staining protocol for flow cytometry can entirely do away with fixation (cell type dependent).

The brefeldin and monensin will help when you want to observe the intracellular production of a protein. They block the intracellular vesicule transportation, so all produced proteins remain in the Golgi system.
To avoid background, you could block the cell after the permeabilization. It is not usual, but you can use different kind of block (since a simple BSA solution to a antibody block, it will depend on the specificity of your antibody).
You could fix the cells after the stainings if you want, or simply don't fix it if you could read it in the same day. It will avoid the morphological change. To permeabilize, the saponin solution (in PBS-BSA) always worked for me.

For intracellar cytokine/protein staining, 0.3% saponin has worked well for me. I block using HBSS+0.5% FBS, and perform all washes in this buffer, with or without saponin, depending on step. Take care to ensure that the saponin powder is white - brown color indicates oxidation, and preparethe perm soln in HBSS+0.5% FBS fresh every expt!