The PAL Key is one of the biggest sources of randomness, lost runs and frustration in MGS1. Shortly after reaching the Underground Base, you lose the PAL Key and have to find it again. Outside of the Big Boss set of categories, the favoured approach is to reenter Underground Base 1 with 11 (or more) Alerts, which causes the card to be in one of seven drainage ditch locations at random.
Players will go west through positions 6 to 1, then if they still haven't found the key, backtrack to position 7 on the other side of the map. Generally positions 1, 2 and 7 (and maybe 3) are considered bad and will often prompt a reset.
Every so often, someone decides to try and figure out a way to manipulate the selection of the key's position through gameplay. The short answer is that you can't - the selection is done using true [pseudo]randomness. The longer answer is that some positions are more likely than others, although it's unlikely to help in practice.
The position selection occurs when you'd expect it to - the moment you enter UGB1. At this point, the game creates an 7-value array where the initial value at index 0 is position 0, index 1 is position 1, and so on. Then, it goes through a simple swapping algorithm:
The random swap index can be the same as the current index - if that happens, no swap occurs. And because a position can be swapped forward, it can be the subject of a swap multiple times.
The randomness is provided (on PC) by Windows' rand() function (with all 7 calls performed in succession), and the game uses modulo arithmetic itself to generate a value 0 to 6. The game on console may use a different random number function.
There's a very small uneven distribution in the RN generator. But moreso, because of how the positions are swapped one after another, earlier positions are more likely to be swapped multiple times. This means some permutations are more likely than others. This would normally create distinct curves on a frequency distribution chart (see further down), but because the game's positions 0 to 6 are not the same as the community's positions 1 to 7, some points are swapped around.
After swapping, these five items are placed at the positions in indexes 0 to 4:
Estimates of PAL Key (left) and Bomb (right) position probability below. X axis: community position numbers. Y axis: approx. probability as a percentage.