Hi,
I would suggest to create a Support case via the https://support.smartbear.com/message/?prod=TestComplete form as it might require further investigation.
If the problem occurs not for all but just for a couple of controls you may try:
a) Use .SetText() instead of .Keys(). (If the control relies on characters to be typed, you may use .SetText() to set the whole required value but the last character and then type this character via the .Keys() method);
b) Store the value to be typed into clipboard and paste clipboard's content into control. Pseudo-code:
var control = <getControl>;
control.SetFocus();
Sys.Clipboard = '<textToType>';
control.Keys('^V');