This isn't an answer to the original question, but rather explains why I don't use the “Equal Symbol Aligned Math Cell”.
Note that I used to use the writing palette to create aligned math, but now I use the solution presented below. And I have some really large notebooks full of typeset maths/physics using this solution.
The Writing Assistant palette contains the button to create an “Equal Symbol Aligned Math Cell” which is actually a GridBox embedded inside of a "Text" cell.
Specifically, it creates
Cell[TextData[Cell[BoxData[
FormBox[GridBox[{{GridBox[{{"\[Placeholder]"}},
GridBoxAlignment -> {"Columns" -> {{"="}}}]}},
GridBoxItemSize -> {"Columns" -> {{Scaled[0.96]}}}],
TraditionalForm]]]], "Text"]
I find this a little hacky and (as mentioned in the comments to the question) a bit unstable.
Luckily, Mathematica has a simpler alignment system built-in.
Just insert a DisplayFormula cell and set the cell alignment
from Left to AlignmentMarker using the
Format ► Text Alignment ► On AlignmentMarker.
Then you can set the formula to align where ever you want, using \[AlignmentMarker\], which can be entered using ⁝am⁝
Cell[BoxData[{
RowBox[{"a", "\[AlignmentMarker]", "=", "b"}], "\[IndentingNewLine]",
RowBox[{RowBox[{"c", "+", "d"}], "\[AlignmentMarker]", "=", "e"}]}],
"DisplayFormula", TextAlignment->AlignmentMarker]
which in TraditionalForm looks like:

Then, if you want, you can make a new cell style that uses this option (or modify an existing style) and assign that style a MenuCommandKey as described in here or in Adam's answer to this question.
Enterinside theEqual Symbol Aligned Math Cellit crashes Mathematica (this is on Windows Vista, Mma V8.0.4). Is anyone else having the same issue? – kglr Jan 28 '12 at 01:14PlaceHolderandEntercombination. HittingEnterinside anyPlaceHolderis crashing Mma. – kglr Jan 28 '12 at 01:24