I have the same problem and called ICA hotline. The answer from the officer is to apply for a visa before you leave Singapore for Malaysia to make sure you have a valid visa to come back to Singapore. I was also told to apply for visa within 14 days in advance of arrival, shouldn't have applied too early.

But I saw a posting by 创世纪 saying "给ICA发了封信,说明需要在哪几天入境,给了新的3个月签证" but dunno how it was done. Pls share your experience here if you manage to get an extension for the visa. Thanks.