Updated 3/31/2013
Since the icons in our apps appear in the normal Android status bar, if you have a phone or an app which has a custom UI (user interface) or an "enhanced status bar", sometimes we "disappear" from the status bar and then our app gets blamed for not working right.
Phones with custom or enhanced status bars know how to reset their own custom features, but they sometimes don't know how to reset us since they are playing by different rules. This is one of the reasons we put in a quick reset option in the Action Bar. Please be aware of this if you have a phone that already has extra fancy status bar features.
Another reason I have discovered lately for our app disappearing from the status bar, is users changing some setting in the "Developer Options" section. Under "Apps" in the "Developer Options" section under "Settings", one option you should not touch and leave at its default setting is "Background process limit". The default is "Standard Limit". Setting it to anything else might have the effect of shutting our app down and wiping us from the status bar if your phone gets low on memory.
Update: 3/18/2013
I notice now that in Jelly Bean 4.1.1, the developer options are all grayed out by default, and you have to turn on a separate switch to even get access to the developer options. Very good idea.
There are also some devices which have some strange quirks. Here is one...
Samsung Galaxy Tab 2
Great tablet, and it works great in landscape mode, but in portrait mode with ICS 4.0.4 it does something that is really annoying. In portrait mode it will only show ONE notification at a time, so our battery level number will constantly be disappearing from the system bar at the bottom if you have other notifications coming in. The solution is to NOT use it in locked down portrait mode only, and if you do use it in portrait mode, if we happen to disappear, to turn the tablet to landscape mode to see the battery level number. Like I said, really annoying.
Update: 3/18/2013
The update to Jelly Bean 4.1.1 cures the "only one notification in portrait mode" problem, and puts the status bar back at the top similar to the Nexus tablets.
There are also so many apps available from so many different sources that it is literally impossible for us to make sure that our app works alongside all of them. All we can really do is play by the Android rules, and hope that others do the same. Unfortunately, there are some apps that don't play by the rules. Some want to take control of other apps. Still others want to completely replace the Android status bar with their own improved version of the status bar.
Here are some examples of apps that seriously mess with us...
Any task manager or app killer/manager
In the newer Android versions you shouldn't need these to control your phone's memory, but if you do use one, make sure that Battery Notifier (Big Text) or Battery Notifier Pro BT are excluded from memory management, otherwise the "manager" might just manage to shut us off.
Handcent SMS / Go SMS
Handcent SMS and Go SMS both can take control of notification sounds. If you let them, then our alarms will not work right, and odd things may happen. Fortunately they allow you to turn this feature off and let the phone handle the sound notifications, which is the way it should be.
StatusBar+
StatusBar+ is more than just a custom status bar. It comes with its own MIUI-style battery bar, the ability to change any and all indicators...
When you see MIUI, think of someone laying a colorful electronic tape over the standard Android status bar. Are you going to see us? Probably not. More on MIUI below...
Chargebar - MIUI battery bar
From Wikipedia:
MIUI (pronounced "Me You I", a play on the common abbreviation of the words user interface as UI), developed by Xiaomi Tech, is an aftermarket firmware for cell phones based on the open-source Android operating system. It features a heavily-modified user interface that does away with the Android app drawer...
"Heavily-modified user interface that does away with the Android app drawer" is all you need to know. If it does away with stock Android features, it might also do away with us.
ICS StatusBar
Start by reading the numerous permissions this app asks for. Also note that Avast is reporting them as malware. Then there's the privacy agreement... "We may disclose your personal information such as an individual's name, postal address, or telephone number, ...Unique identifiers such as email address, site user name and password."
Swipepad: Hyperspace Jump
Last time I saw it, Swipepad had one of the scariest user agreements I've ever read, basically saying it's not their fault if you get a virus, and that you use it at your own risk.
I can't say this enough... Please, take time to read those permissions and user agreements.