Don't know so much about a blinking red light, do you mean amber? If so, my research's shown that, yes, your device isn't charging, and there is the possibility that your battery is overheating. From what I understand, so as not to damage the device and/or battery, if the battery gets too hot, it'll no longer charge. Given enough time like this, you'll find that not only is your device not charging, but it's actually having it's battery drained. I'd started leaving the keyboard slid out, and placing the device somewhere in the open, as opposed to a corner of the desk, or too near my notebooks exhaust fans (especially when using WiFi (WMWifiRouter, specifically)), and hadn't gotten the prob in some time since.
Peace, Pimpin'.
BTW, I think it's so F^&#in' STUPID that HTC'd made the Mogul in such a way that the battery MUST be in the device to function. If the device could use a different power source, then ya wouldn't have to worry about the battery overheating (ie: Using your device as a wireless AP w/ WMWiFiRouter, no battery, and plugged into the wall). A workaround for this would be bitchin'. Any input anyone?