I see the exact same issue in our VC 2.5 Update 1 / ESX 3.5 deployment. Here is what I am seeing.
I am running VC 2.5 on a dedicated physical host, specifically a HP Proliant DL380G2 with 6GB of memory. I am pointing to a seperate SQL DB server, also dedicated to hosting this single database instance. The SQL server is a HP DL380G5 quad core with 16GB of memory. I am running VC 2.5 Update 1, build 84767. This is a very lightly loaded lab environment with a small number of hosts, 4, and only 16 Winows 2003 Server virtual machines spread between 4 hosts. Two of the ESX hosts are 3.5 Update 1 (build 84374), the other two are 3.0.2 (build 63195). I am running SQL 2005 SP2 64-bit.
The gaps in data appear for all 4 counters: CPU, Memory, Disk and Network, but only if you look at "Past Day". Any other time frame, such as Real Time or Past Week, I see no gaps.
I have verified that this is occuring for Statistics Level 1 and 2. (VC 2.5 appears to have no setting for "Statistics Collection Thread Limit" as VC 2.0.x did).
The gaps appear for data on ESX hosts as well as individual VMs. The gaps appear on ESX 3.5 (build 84374) hosts and their VMs, as well as ESX 3.0.2 (build 63195) hosts and their VMs. The gaps appear to be occuring aproximately once per hour for about 5 minutes.
Also, this is a complete new install of VC 2.5 and the SQL database. I have re-installed VC 2.5 Update 1 specifing a re-initialized database (deleting any previous DB). The problem persists.