Just to be clear, most of my dialogs still work fine.
I just have one which is behaving oddly. First of all, I have a main configuration dialog which opens and displays its buttons fine. One of those buttons has a menu which then opens another dialog and this is where the problem happens. Both dialogs are modal.
As you can see from this gif, they are invisible on startup and only appear when moving the mouse over them. Reloading my list control from clicking the presets button menu makes the buttons disappear again.

This is the relevant bits of my resource file...
IDD_DIALOG_CONFIGURE DIALOGEX 0, 0, 620, 400
STYLE DS_SETFONT | WS_MAXIMIZEBOX | WS_POPUP | WS_CAPTION | WS_SYSMENU | WS_THICKFRAME
CAPTION "Configuration"
FONT 8, "Segoe UI", 400, 0, 0x0
BEGIN
CONTROL "", IDC_SCINTILLA, "Scintilla.jsp4", WS_CLIPCHILDREN, 0, 0, 620, 374
PUSHBUTTON "Code", IDC_BTN_CODE, 7, 380, 50, 14
PUSHBUTTON "Style", IDC_BTN_STYLE, 64, 380, 50, 14
PUSHBUTTON "Samples", IDC_BTN_SAMPLES, 121, 380, 50, 14
DEFPUSHBUTTON "&OK", IDOK, 455, 380, 50, 14
PUSHBUTTON "&Apply", IDC_BTN_APPLY, 509, 380, 50, 14
PUSHBUTTON "&Cancel", IDCANCEL, 563, 380, 50, 14
END
IDD_DIALOG_STYLE DIALOGEX 0, 0, 330, 200
STYLE DS_SETFONT | DS_MODALFRAME | WS_POPUP | WS_CAPTION | WS_SYSMENU
CAPTION "Editor Properties"
FONT 8, "Segoe UI", 400, 0, 0x0
BEGIN
CONTROL "", IDC_LIST_STYLE, "SysListView32", LVS_ALIGNLEFT | WS_BORDER | WS_TABSTOP, 0, 0, 330, 256
PUSHBUTTON "&Import", IDC_BTN_IMPORT, 7, 180, 50, 14
PUSHBUTTON "&Export", IDC_BTN_EXPORT, 64, 180, 50, 14
PUSHBUTTON "&Presets", IDC_BTN_PRESETS, 121, 180, 50, 14
PUSHBUTTON "&Close", IDCANCEL, 273, 180, 50, 14
END
I've attached the source of the dialogs.
CDialogConfigure is the main window where the buttons are fine and CDialogStyle is the one with the disappearing buttons.
And for more hilarity, I can open other dialogs from CDialogConfigure such as a find/replace dialog and GOTO line dialog - the buttons in these are fine.
Reverting the SDK changes fixes it so I really have no idea what is going on.