the attached math-example from 1.1.6fix3 is an eqnarray, which is by default left-center-right justified. opening with 1.2.0 gives always center Herbert -- http://www.educat.hu-berlin.de/~voss/lyx/
#LyX 1.1 created this file. For more info see http://www.lyx.org/ \lyxformat 218 \textclass article \language german \inputencoding latin1 \fontscheme default \graphics default \paperfontsize 10 \spacing single \papersize a4paper \paperpackage a4 \use_geometry 0 \use_amsmath 0 \paperorientation portrait \secnumdepth 3 \tocdepth 3 \paragraph_separation indent \defskip medskip \quotes_language german \quotes_times 2 \papercolumns 1 \papersides 1 \paperpagestyle default \layout Standard \begin_inset Formula \begin{eqnarray} v_{i} & = & \left\{ \begin{array}{cc} 1 & \textrm{für }i\in \{1,2,9,16\}\\ 2 & \textrm{andernfalls} \end{array}\right. \nonumber \\ PC1:\, \{0,1\}^{64} & \rightarrow & \{0,1\}^{28}\times \{0,1\}^{28}=C\times D\\ PC2:\, C\times D=\{0,1\}^{28}\times \{0,1\}^{28} & \rightarrow & \{0,1\}^{48} \end{eqnarray} \end_inset \the_end