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Seems lot of people think that employee employer relation is not major reson behind 221G. But in fact it is main reson behind it. They are giving 221G, and it means administrative processing. They will request uscis to review H1B approval again through this administrative processing. And some time uscis even cancel approved H1B. I dont want you to scare, but it is fact. Situation in nepal doesn't seems to bad as in india.
Regarding PIMS, yes it is one reason behing 221G. But it can be easily avoided by sending email to consulate with your copy of approved H1B document and requesting them to initiate PIMS verification.
http://www.murthy.com/news/n_h14ind.html
See the link above about murthy law firm analysis for 221G, and they think that it a lot to do with Emp-Empo relation memo. And uscis haven't pull it back yet.
And yes even though, E-E relation is major issue while applying, uscis mentions that it should me maintained through out the validity period
of H1B. If they think you didn't maintain it, they can revoke it. See uscis link below. Well i dont want to scare you, a lot of my friends went and get stampped easily and few got stuck also. So, dont get scared but informed and prepare for worst.