Yeah, the MLV format is designed to have frames appear out-of-order to be able to optimize memory block and write sizes.
Nevertheless it is simple to overcome this - there is a .idx file which contains the file numbers and offsets to VIDF blocks.
These file can be generated using mlv_dump or with the in-camera player.

If you can send me the direct link to the API the mlv routines have to fulfill, i can prepare what is necessary to index the files on startup etc.

see https://bitbucket.org/hudson/magic-lantern/src/tip/modules/mlv_rec/mlv.h...

typedef struct {
uint16_t fileNumber; /* the logical file number as specified in header */
uint16_t empty; /* for future use. set to zero. */
uint64_t frameOffset; /* the file offset at which the frame is stored (VIDF/AUDF) */
} PACKED mlv_xref_t;

typedef struct {
uint8_t blockType[4]; /* can be added in post processing when out of order data is present */
uint32_t blockSize; /* this can also be placed in a separate file with only file header plus this block */
uint64_t timestamp;
uint32_t frameType; /* bitmask: 1=video, 2=audio */
uint32_t entryCount; /* number of xrefs that follow here */
//mlv_xref_t xrefEntries; /* this structure refers to the n'th video/audio frame offset in the files */
} PACKED mlv_xref_hdr_t;