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.
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The [Writing Assistant palette][1] 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][2] and set the cell alignment
from `Left` to `AlignmentMarker` using the
[`Format ► Text Alignment ► On AlignmentMarker`][3].
Then you can set the formula to align where ever you want, using [`\[AlignmentMarker\]`][4], 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][5] or in [Adam's answer][6] to this question.
[1]: http://www.wolfram.com/broadcast/screencasts/writingassistant/
[2]: http://reference.wolfram.com/mathematica/ref/menuitem/InsertNewCell.html
[3]: http://reference.wolfram.com/mathematica/ref/menuitem/TextAlignment.html
[4]: http://reference.wolfram.com/mathematica/ref/character/AlignmentMarker.html
[5]: https://stackoverflow.com/a/4211050/421225
[6]: https://mathematica.stackexchange.com/a/815/34