There appears to be a bug in mkiv with greek letters (and other math symbols?) within ppchtex. I am using the latest conTeXt minimals:
(This is LuaTeX, Version snapshot-0.35.0
ConTeXt  ver: 2009.01.18 14:39 MKIV  fmt: 2009.2.24  int: english/english)


(Almost) minimal example (and attached pdf results).

\enableregime[utf]
\usemodule[chemic]

\starttext
\startTEXpage
	\startchemical[width=fit,height=fit]
		\chemical[ONE,Z0,MOV1,SB5,Z0][C_{\alpha},C_α]
	\stopchemical
\stopTEXpage
\stoptext

(Under mkiv, the \alpha becomes an ff ligature)