I'm pretty sure my problem is unique.
I'm using OpenJDK 7 to play Minecraft, in order to avoid wrangling with Wine. Recently, this setup has started to give me problems.
I am getting "System program problem detected" error dialogs, and prompts to send error reports to Apport. This happens even when I'm not playing MC - I'll see it at startup, for example - but I get one of these dialogs several times an hour when I play. Moreover, every so often, the game will freeze. Sometimes the event will be identical to a lag spike, but some of the time, something really weird will happen to my computer:
It briefly flashes through all the windows that I have up, and then settles on a single one - Google Chrome, usually - and both the dashboard and the info-bar along the top of the screen will vanish. I'll still be able to use whatever window it settles on, but I won't be able to switch between windows, or do anything that involves the dash, and the only way to restart my computer is to hard-reboot by holding down the power button. I don't know if keyboard shortcuts for switching windows, etc. work, mostly because I don't know the keyboard shortcuts. This has not happened so far when I'm NOT playing Minecraft.
I have been trying to use several mods, listed below, and installing them using MCPatcher 3.0.3; I'm pretty sure that the problems started when I used MCPatcher to install Optifine and ModLoader at the same time, and had a file conflict. It happens even after I removed all mods from the jar, and after "force updating"; I'm currently experimenting with using MCPatcher to completely un-patch the game. So far, I have experienced the lag-spikes, but it hasn't crashed my computer yet. If it turns out that it doesn't work, I'll try getting a fresh jar file. I will provide updates as they come by editing the post.
Mods: Single Player Commands - version 4.6 (I don't know if this can actually be installed with MCPatcher.) TooManyItems for 1.5.1 (includes Mar 23, 2013 as a date; I don't remember if that's when I downloaded it or if it's something else, although it's probably the former) Timber! (1.5.1) ModLoader (as far as I know, it's for 1.5.1. I should make sure of that.) Optifine 1.5.1 HD B3
Does anyone have any idea what is happening to me?