Sometimes notation gets auto-converted from traditional to raw input and won't convert back

Question

For example, I'm typing this:

When upon hitting the last character it gets converted to:

And trying to Convert To TraditionalForm has no effect. This glitch has happened a few times and on different characters each time. Is there a reason for this happening?

EDIT - By request from Mr. Wizard, here is the Cell Expression (and what was displayed) of the cell to which this just happened.

What was displayed:

Subscript[
Overscript[u, .], 
  t] = \[DifferentialD]Subscript[u, t]/\[DifferentialD]t\[InvisibleComma], 
 where Subscript[u, \[Placeholder]]

Cell Expression:

Cell[TextData[Cell[BoxData[
 FormBox[
  RowBox[{
   RowBox[{
    RowBox[{"Subscript", "[", "\n", 
     RowBox[{
      OverscriptBox["u", 
       StyleBox[".",
        FontWeight->"Bold"]], ",", " ", "\n", "  ", "t"}], "]"}], " ",
     "=", " ", 
    RowBox[{
     RowBox[{"\[DifferentialD]", 
      RowBox[{"Subscript", "[", 
       RowBox[{"u", ",", " ", "t"}], "]"}]}], "/", 
     RowBox[{"\[DifferentialD]", "t"}]}]}], "\[InvisibleComma]", 
   RowBox[{",", " ", "\n", " ", 
    RowBox[{"where", " ", 
     SubscriptBox["u", "\[Placeholder]"]}]}]}], TraditionalForm]],
 FormatType->"TraditionalForm"]], "Outline5",
 CellChangeTimes->{{3.5589693713435035`*^9, 3.5589693812760715`*^9}, {
   3.5589694358751945`*^9, 3.5589694980697517`*^9}, {
   3.5589695385210657`*^9, 3.5589695520988417`*^9}, {
   3.5589695873348575`*^9, 3.558969609079101*^9}, {
   3.5589701806157913`*^9, 3.5589702522708893`*^9}, 
   3.5589703063239813`*^9, {3.558990416805235*^9, 
   3.5589904721864023`*^9}}]