I found several references to disappearing controls in VS2003, but they all said the problem had been fixed in VS2005.
The cause of this turned out to be that some lines had removed themselves from the designer.cs file :-
///
/// formMyForm
///
this.AutoScaleDimensions = new System.Drawing.SizeF(6F, 13F);
this.AutoScaleMode = System.Windows.Forms.AutoScaleMode.Font;
this.AutoSizeMode = System.Windows.Forms.AutoSizeMode.GrowAndShrink;
this.ClientSize = new System.Drawing.Size(869, 717);
this.Controls.Add(this.splitContainer1);
this.Controls.Add(this.buttonOK);
this.Controls.Add(this.buttonCancel);
this.Controls.Add(this.buttonAccept);
this.Name = "formMyForm";
this.Text = "My form title";
Copying these lines from the version in source control seemed to restore all the controls in the dialog.