Just for background...
Chkdsk is a utility that will scan the file allocation tables for incosistencies and report them - if the /f (fix) option is used it will attempt a repair which usually results in orphaned clusters being put in a folder named FIX.XXX (xxx is an incrementing number depending times run and on if fix.000 is there etc) - these clusters will be broken down into logical groups into files recovered.xxx etc.
chkdsk does not care or look at partitions - so dont get confused with the partition scheme across disks - it only looks at the file system within a partition.
Partitioning:.....
You can grow (and maybe shrink - not tried that ) paritions however..... if you have allocated a 1gb partition and there is a file occupying space near the upper boundry of the partition you will not be able to shrink the partition as the space is considered in use. To get around this if you use a defragmentation utilitly to place all the clusters consecutively near the bottom end of the partition you should be able to shrink the partition to make available space for another partition.
Drive lettering (yes a red herring)....
If I recall correctly from the DOS days on how the letters are initially assigned it will be C: is your primary boot partition and then the rest are assigned on the principle of the next letters used will be primary partitions on subsequent drives e.g. if you have 1 additional physical drive the primary partition on that will default to D: (if 2 E: will be the next primary partition) and then it will go through allocating letters in order of secondary partitions from the first drive onwards.
So in the example of 2 disks with disk 1 having a primary and secondary partition and disk 2 only having a primary partition the scheme would be C: being your boot partition on disk 1, D: the primary partition on disk 2 and E: the secondary partition on disk 1.
This is all pretty much by the by as you can use the disk manager in XP/vista/W7 to reallocate the drive letters to what you like - so in the example you could change D: to F: temporarily - assign E: to D: (as it is now not in use) and then change f: to E:.
As you can see from the above your restore partition has not moved but has just been allocated a different identifier.
Back to the original question of chkdsk and whether it reports something that is not there: -
If chkdsk is reporting a problem and cannot fix it then it will keep on reporting the problem endlessly - the fact that it is running is an indication that you are using a file system it supports as it would terminate otherwise.
If this is going to be a new install then re-format the partition as it sounds like you could have a dodgy cylinder on the disk (e.g. a correction is written by chkdsk but is not read back as being corrected). DO NOT do a quick format as this will only re-write the file allocation table with a blank one, if you do a full format which will take longer it will verify the sectors as it goes and allocate out those that are bad in the file allocation table.
This could be an indication that the disk itself is on its way out and may need replacing soon - so some advice would be to make sure anything critical on this physical disk is backed up.